VaxLab: integrated platform for rapid multistrategy mRNA vaccine design

Abstract mRNA vaccine efficacy depends on sequence optimization, but designing optimal sequences is challenging due to complex cellular RNA regulatory mechanisms. Here we present VaxLab, an open-source web platform that provides the complete design-to-synthesis workflow for mRNA vaccines in a unified interface. VaxLab incorporates four codon optimization algorithms based on distinct approaches: codon usage matching, secondary structure design and deep generative models. 5′ and 3′ untranslated regions can be designed using provided generative models or selected from a predefined sequence library. The designed sequences are then evaluated and reported for ten predictive metrics for RNA stability, protein expression and manufacturing risks. An integrated sequence editor with annotation tools enables further adjustments, and final sequences are exported in formats compatible with commercial DNA synthesis services. We validated VaxLab using influenza hemagglutinin sequences, completing the full design workflow in under 5 min per variant. In HCT116 cells, optimized variants showed up to 9.5-fold differences in protein expression, with most achieving at least 2.9-fold higher expression than the wild-type sequence. VaxLab provides an integrated optimization workbench that accelerates mRNA vaccine design by enabling principled selection among multiple optimization techniques informed by current understanding of RNA regulation.