Biologics, small molecules, DNA therapeutics, radiopharmaceuticals: how modality shapes your development plan

Modality decides which nonclinical guideline governs your program, which animal species you test in, how you set a starting dose, whether immunogenicity is a central risk, and how fragile your supply chain is. Small molecules follow ICH M3(R2), biologics follow ICH S6(R1), oncology programs overlay ICH S9, and oligonucleotides and radiopharmaceuticals borrow from these under their own FDA guidances. Plan around those differences from day one.

Which nonclinical safety guideline governs my program?

Small molecules sit under ICH M3(R2), adopted by FDA in January 2010 [1]. It calls for repeat-dose toxicology in a rodent and a non-rodent, a core genotoxicity battery, and safety pharmacology before first-in-human dosing [1]. It excludes biotechnology-derived products, which fall under ICH S6 [1].

Biologics follow ICH S6(R1), adopted by FDA in May 2012 [2]. Its central concept is the relevant species, and two are the default for short-term studies. One species is justified when the candidate is active in only one, standard genotoxicity studies are not needed, and 6-month chronic studies are considered sufficient for chronic-use products [2].

Oncology overlays ICH S9, issued by FDA in March 2010, which applies to small molecules and biopharmaceuticals in patients with advanced cancer and limited options [3]. It drops stand-alone safety pharmacology and pre-trial genotoxicity, and it treats 3-month repeat-dose studies as sufficient to support marketing for most advanced-cancer indications [3].

Oligonucleotides have no ICH guideline of their own, though ICH S13 is now in development. A 2023 review notes that M3(R2), written for small molecules, has applied by default [4]. FDA finalized a clinical pharmacology guidance for oligonucleotides in June 2024 [5] and drafted a nonclinical safety guidance in November 2024 that says these products differ in many regards from small molecules and therapeutic proteins [6].

Therapeutic radiopharmaceuticals follow FDA's August 2019 oncology guidance, which supplements S9 [7]. It separates radiation toxicity, addressed by an animal biodistribution and dosimetry study, from ligand toxicity, addressed by toxicology of the non-radioactive "cold" pharmaceutical in one species [7]. Diagnostic radiopharmaceuticals fall under 21 CFR Part 315 [8].

How does modality change the starting dose?

For small molecules in healthy volunteers, FDA's 2005 guidance converts the animal no-observed-adverse-effect level to a human equivalent dose by body surface area and divides by a default safety factor of 10 [9]. It notes that mg/kg scaling may suit monoclonal antibodies better than surface-area conversion [9].

ICH S9 says a NOAEL is not essential for anticancer drugs and describes starting at 1/10 of the dose severely toxic to 10 percent of rodents, or 1/6 of the highest non-severely toxic dose in non-rodents [3]. M3(R2) adds a microdose route: exploratory trials at 100 micrograms or less with a reduced nonclinical package [1].

Radiopharmaceuticals split the dose in two. Administered activity is set from animal biodistribution and estimated absorbed radiation dose to human organs, with a relative biological effectiveness of 5 applied to alpha emitters [7]. The cold ligand's mass dose comes from its own toxicology [7]. For diagnostics, FDA’s 2018 microdose guidance applies at total doses of 100 micrograms or less [12], and 21 CFR 315.6 says a maximum tolerated dose need not be established [8].

How does immunogenicity differ across the four modalities?

For therapeutic proteins, immunogenicity is central. FDA's 2014 guidance describes consequences from loss of efficacy to neutralizing antibodies that cross-react with an endogenous protein, and calls for a risk-based assessment of aggregates, impurities, glycosylation, and formulation [13]. S6(R1) adds that animal anti-drug antibody data do not predict human immunogenicity [2].

Oligonucleotides carry a different profile. FDA's 2024 guidance asks sponsors to assess responses to carrier, backbone, sequence, and novel epitopes, and to measure innate immune activation when sequences contain motifs such as CpG [5]. Phosphorothioate antisense drugs can activate the alternative complement pathway, and roughly 40 percent of evaluated sequences lowered platelets in non-human primates versus 20 percent in humans [4].

Aptamers sit at the low end, with immunogenicity characterized as none or low against the high, dose-accumulating immunogenicity of antibodies [10]. However, when aptamers are engineered with PEG or other conjugate components, those components carry their own immunogenicity risk, and FDA’s risk-based approach can still call for antibody assays [13]. For radiopharmaceuticals the question belongs to the ligand, whose toxicities are usually minor [7].

What does modality do to CMC and supply chain?

Biologics are made by living cells, so the product is partly defined by its process. FDA lists aggregates, impurities, and glycosylation variants as product-related immunogenicity risks, which makes a manufacturing change a safety question, not only a quality question [13]. On the biologic I carried to IND acceptance, comparability between research-grade and GMP material sat on the critical path from the start.

Oligonucleotides and aptamers come from solid-phase chemical synthesis, with low batch-to-batch variation and no cell-derived contaminants [10]. Their liability is pharmacokinetic: unmodified aptamers have in vivo half-lives under 10 minutes, so PEGylation and 2'-sugar modifications are part of the design [10]. Only two aptamers are approved, pegaptanib in 2004 and avacincaptad pegol on August 4, 2023 [10], [14].

Radiopharmaceuticals have the hardest supply problem. Lutetium-177 decays with a 6.65-day half-life, comes from about ten aging research reactors, and has no feasible production route without neutron irradiation [11]. FDA also requires the entire decay cascade, including daughter radionuclides, in biodistribution and dosimetry [7].

Which FDA center reviews my product, and does it matter?

On June 30, 2003, FDA moved monoclonal antibodies for in vivo use and most therapeutic proteins, including cytokines and enzymes, from CBER to CDER; CBER kept cellular products, gene therapy, vaccines, and blood products [15]. All four modalities in this article are therefore reviewed in CDER, in divisions organized by therapeutic area rather than modality.

FDA's 2024 oligonucleotide guidance places aptamers out of scope because they act by direct modulation of proteins [5], yet avacincaptad pegol was approved as a CDER novel drug [14]. A division's depth with your modality varies, and the pre-IND meeting is where you learn how much context the IND must supply.

What surprised me moving between modalities?

Moving from small molecules to a biologic, the surprise was how much hinged on one species question. Once pharmacologic relevance was established, the toxicology design followed S6(R1) rather than a rodent-plus-dog default, and the budget changed with it. That first-in-class biologic for a rare pediatric leukemia reached IND acceptance, with Fast Track designation two months later.

With aptamers, the cleanest manufacturing in the portfolio came with the least forgiving pharmacokinetics. With radiopharmaceuticals, dosimetry replaced much of toxicology, and the limiting reagent was the calendar. The constant was a modality-specific bioanalytical plan validated before first dose. The limits are real: guidelines set floors, reviewers can ask for more, and antibody-drug conjugates borrow from two frameworks at once [2].

This article is part of the Product Development Services practice at Hamilton Atlas Group — see the full capability list there.

References

1. U.S. Food and Drug Administration. M3(R2) Nonclinical Safety Studies for the Conduct of Human Clinical Trials and Marketing Authorization for Pharmaceuticals. FDA, 2010.
2. U.S. Food and Drug Administration. S6(R1) Preclinical Safety Evaluation of Biotechnology-Derived Pharmaceuticals. FDA, 2012.
3. U.S. Food and Drug Administration. S9 Nonclinical Evaluation for Anticancer Pharmaceuticals. FDA, 2010.
4. Goyenvalle A, Jimenez-Mallebrera C, van Roon W, et al. Considerations in the Preclinical Assessment of the Safety of Antisense Oligonucleotides. Nucleic Acid Therapeutics. 2023;33(1):1-16.
5. U.S. Food and Drug Administration. Clinical Pharmacology Considerations for the Development of Oligonucleotide Therapeutics. FDA, 2024.
6. U.S. Food and Drug Administration. Nonclinical Safety Assessment of Oligonucleotide-Based Therapeutics. FDA, 2024.
7. U.S. Food and Drug Administration. Oncology Therapeutic Radiopharmaceuticals: Nonclinical Studies and Labeling Recommendations Guidance for Industry. FDA, 2019.
8. Legal Information Institute, Cornell Law School. 21 CFR § 315.6 - Evaluation of safety. LII, 2026.
9. U.S. Food and Drug Administration. Estimating the Maximum Safe Starting Dose in Initial Clinical Trials for Therapeutics in Adult Healthy Volunteers. FDA, 2005.
10. Zhou J, Rossi J. Aptamers as targeted therapeutics: current potential and challenges. Nature Reviews Drug Discovery. 2017;16(3):181-202.
11. Vogel WV, van der Marck SC, Versleijen MWJ. Challenges and future options for the production of lutetium-177. European Journal of Nuclear Medicine and Molecular Imaging. 2021;48(8):2329-2335.
12. U.S. Food and Drug Administration. Microdose Radiopharmaceutical Diagnostic Drugs: Nonclinical Study Recommendations Guidance for Industry. FDA, 2018.
13. U.S. Food and Drug Administration. Immunogenicity Assessment for Therapeutic Protein Products. FDA, 2014.
14. U.S. Food and Drug Administration. Novel Drug Approvals for 2023. FDA, 2023.
15. U.S. Food and Drug Administration. Transfer of Therapeutic Biological Products to the Center for Drug Evaluation and Research. FDA, 2003.