Scalable Production of a De Novo SARS-CoV-2 Antiviral Miniprotein in Escherichia coli

Abstract

Background/Objectives: The rapid emergence of SARS-CoV-2 variants that evade neutralizing antibodies underscores the need for new antiviral biologics that integrate precise molecular design with scalable, cost-effective manufacturing. Computationally designed miniproteins targeting the spike protein’s receptor-binding domain (RBD) offer a promising alternative to monoclonal antibodies because of their small size, high thermal stability, and compatibility with microbial expression systems. Here, we detail the full development and cGMP manufacturing of IPD-52520, a novel antiviral miniprotein produced using an optimized E. coli platform. Methods: Two candidate miniproteins, a homotrimeric construct (Trimer, IPD-52520, 17 kDa) and a tandem fusion construct (Daisy, IPD-52521, 25 kDa), were evaluated in parallel through systematic optimization of strain selection, media formulation, fed-batch fermentation, inclusion-body solubilization, refolding, and chromatographic purification. The leading candidate was scaled from 5 L to 50 L under cGMP conditions, and biophysical and stability analyses were conducted to support nonclinical and Phase 1 clinical development. Results: The Trimer was selected as the lead molecule based on superior preclinical efficacy, favorable pharmacokinetics, and higher volumetric yields. The optimized process yields about 2 g/L of purified protein at over 90% purity. Scale-up from 5 L to 50 L demonstrated excellent batch consistency across six independent runs. Biophysical studies confirmed a well-folded, predominantly alpha-helical trimer (Tm = 73.4 °C; polydispersity = 1.005) with an intact primary structure and strong target binding (KD < 1 pM). Stability studies show the drug remains stable at 2–8 °C for at least 12 months, with ongoing long-term studies. Conclusions: These findings demonstrate that computationally designed antiviral miniproteins can be translated into scalable biologics and establish a platform for rapid therapeutic development against current and future pandemics.