Main Conference Day 2Wednesday, 12 November 2025 - CET (Central European Time, GMT+01:00)

Both early and late phase process optimization play critical roles in successful project management. Early phase projects are often driven by speed and therefore the focus of optimization is either on new, often challenging, building blocks or on new chemistries that deviate from standard oligonucleotide synthesis protocols. Conversely, late phase optimization is driven by quality factors, cost reduction, scalability and efficiency. At this stage plenty of process data and real-world evidence are available. Therefore success rate of process enhancement is based on actual performance metrics.

2’-N-methylacetamide (NMA) nucleotides are a novel type of monomer for splice modulating Antisense Oligonucleotides (ASOs). Recently, a sequence consisting of 18 NMA nucleotides was developed and manufactured at scales up to 163 mmol. Despite the seemingly inert nature of the 2’ NMA functionality, it is prone to engaging in side reactions that result in the formation of late-eluting impurities (LEI), which are challenging to control without negatively impacting coupling completion. Ultimately, LEI were mitigated by judicious choice of the amidite to activator ratio used in coupling. Targeted capping steps were introduced in select elongation cycles that were prone to generating deletion impurities, thereby reducing the incidence of deletion impurities with minimal introduction of capping related impurities. Additionally, it was necessary to develop a new cleavage and deprotection protocol to control the rate of NMA related cleavage products, as well as impurities related to the addition of methylamine to the ASO. Described herein is a summary of development efforts and the first on-scale manufacture of a 2’-NMA functionalized ASO.

At Wave Life Sciences, stereopure oligonucleotides containing chimeric phosphorothioate (PS), phosphoryl guanidine (PN) and phosphodiester (PO) backbones are rationally designed to optimize pharmacology and efficacy. Our methods enable synthesis of stereopure oligonucleotides with PS and PN linkages, therefore the configuration of each linkage must be confirmed as part of identity testing. We will describe approaches to confirm stereochemical identity of the oligonucleotide with an emphasis on confirming configuration using chromatography and enzymatic digestion in addition to the standard techniques of Mass ID and MS/MS sequencing.

We report a programmable, pH-controlled strategy for site-selective cysteine modification in peptides using triazine-thiol exchange. Internal or N-terminal cysteines can be site-selectively modified via dynamic covalent chemistry. We have supported our mechanistic model with both, experimental and computational studies, enabling precision peptide engineering through tunable, mechanism-guided cysteine functionalization.

Protein–protein interactions (PPIs) represent promising but underexploited targets in drug discovery and development due to the challenging landscapes of their extensive contact interfaces. The identification of reactivity hotspots within these interfaces by electrophile scanning facilitates the design of covalently binding peptides with enhanced potential as PPI inhibitors.

Extracorporeal membrane oxygenation (ECMO) is a form of life support for critically ill patients with severe respiratory or cardiac failure. However, interactions between patient blood and ECMO biomaterials increase the risk of thrombosis, necessitating concurrent anticoagulation treatment, with the standard of care being heparin. Here we describe the use of mRNA display based discovery using a cyclotide scaffold to develop a factor XII inhibitor as a selective anticoagulant that offers a potential alternative to heparin in ECMO treatment.

Oligonucleotide therapeutics, expanding from rare diseases to more prevalent conditions, have increased demand for GMP-manufactured oligonucleotides and acetonitrile. The acetonitrile supply chain is volatile due to economic, regulatory, and environmental factors, affected by crises such as the 2008-2009 financial crash and COVID-19. Addressing these issues necessitates strategic planning, recycling method diversification, and regulatory compliance. A risk assessment process evaluated potential waste contamination in recycled acetonitrile, categorizing contaminants by severity and probability.

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This presentation will discuss how peptides unlock a completely new possibility for dissolving neurotoxic protein aggregates, which are a hallmark to various neurodegenerative disorders. The development of PRI-002 from discovery to phase II in Alzheimer’s disease will be presented.

The translation of complex therapeutics from discovery to development presents unique hurdles for innovators. Emerging modalities like oligonucleotides and peptides face a 73% attrition rate in early development (Nature Reviews Drug Discovery, 2023), driven by critical bottlenecks in: 1) Structural Fidelity - Ensuring pharmacophore integrity through scale-up; 2) Impurity Snowball Effect – Uncontrolled process-related variants leading impurity accumulation beyond thresholds and 3) Manufacturing Discontinuity –Knowledge gaps between discovery synthesis and GMP production. Through anonymized case studies of clinical-stage programs, this talk will dissect how integrated technical strategies can address these translational cliffs, and how a cross-functional convergence framework, where medicinal chemistry insights and process science fundamentals strategically align, enables synchronized progression of oligonucleotide/peptide candidates.

Oligonucleotide therapeutics purification relies heavily on preparative-scale chromatography. Reverse phase high performance liquid chromatography (RP-HPLC) and anion exchange chromatography (AIEX) are the most widely employed techniques. This presentation will highlight oligonucleotide purification approaches using reverse phase and anion exchange DuPont™ AmberChrom™ resins. It will cover various oligonucleotide modalities, purification approaches, and introduce a new high-loading anion exchange resin for oligonucleotide and peptide purification.

Solid Phase Peptide Synthesis (SPPS) is efficient but generates significant solvent waste. Tag-Assisted Peptide Synthesis (TAPS) offers a greener, solution-phase alternative using soluble tags. We present a continuous TAPS process using aqueous washes after each cycle in a green solvent system, reducing organic solvent use by 90% and reagent excess by >50%, while maintaining product quality—establishing TAPS as a sustainable alternative to SPPS.

The development of siRNA fixed-dose combinations (siRNA FDCs) presents intrinsic formulation and analytical challenges. Key hurdles include distinguishing and quantifying the two siRNAs and their product-related impurities. To assess purity and accurate quantification, orthogonal chromatographic techniques like ion-pairing reversed-phase chromatography (IP-RP-LC) under both denaturing and non-denaturing conditions, as well as denaturing anion-exchange chromatography (AEX), are employed. Mass spectrometry plays a crucial role for the identification and peak purity evaluation. Establishing a comprehensive analytical toolbox for both physical and chemical characterization is essential to assess the feasibility of FDC formulations. By thoroughly designing the analytical assessment strategy, the quality and efficacy of siRNA FDC drug products can be assured.

Method transfer case studies for the oligo assay/impurity methods by IP-RP-UHPLC will be presented. The learnings will include how to address the issues associated with the sensitivity, resolution, linearity, and method precision during the method transfer on different LC systems (Vanquish, Agilent and Waters) at different CDMOs. The cases indicate it is crucial to establish the procedures for the LC system cleaning/maintenance to ensure the successful method transfer and routine use later.