While viruses tirelessly reinvent themselves to optimize infection and immune evasion, including refining their signal peptides to optimize viral replication in the secretory pathway, the understanding and the ability to engineer viral signal peptides for biotechnology remains limited. In viruses such as HIV and SARS-CoV-2, mutations in the N-terminal sequences reshape infectivity, antigen presentation, and antibody escape.
How SARS-Cov-2 signal peptide mutations enable vaccine evasion
A compelling study from 2021 (1) provided new insights into signal peptide-based mechanisms that allow the virus to evade neutralizing antibodies, prompting new requirements for vaccines. The study found that Epsilon variant mutations were responsible for rearrangements in critical areas of the spike glycoprotein: one affecting the receptor binding domain, and two impacting the N-terminal domain of the spike glycoprotein.
This mechanism underlines an important but still underappreciated aspect of signal peptide function: their role is often larger than simply acting as address labels for protein targeting. Instead, in many instances, they can influence signal peptide cleavage accuracy, protein glycosylation patterns, disulfide bond arrangements and ultimate protein folding.
For biologics development, this demonstrates that signal peptide choice can affect product quality, immunogenicity, and even structural integrity – not just expression levels.
HIV: The dual effect of signal peptides
Also HIV is known for its ability to optimize signal peptides to modulate antigenicity and interactions with the immune system, resulting in a dual effect: increased immune evasion as well as improved transmission (2).
Studies have demonstrated that replacing the native HIV-1 signal peptide with alternative signal peptides can significantly affect antigenicity and immunogenicity. These modifications can alter folding and glycosylation, leading to changes in how the immune system recognizes the protein (3).
These studies demonstrate the importance of signal peptide optimization for HIV vaccine development, influencing the structural and antigenic properties of the Env protein. Understanding signal peptide mechanisms will enable the design of vaccines that elicit more effective immune responses against HIV.
The neglected diversity of signal peptides in drug development
Most biologics development focuses on optimizing expression using a handful of well-known signal peptides (like tPA or IL-2), possibly ignoring thousands of other unique evolutionary solutions found in nature and viruses, as well as synthetic signal peptides emerging from computational approaches. This conservatism risks overlooking more efficient and immunologically effective designs.
Today, analyzing thousands of signal peptides in parallel is possible using a combination of computational and wet lab methods. For example, Avenue Biosciences’ platform evaluates over 5,500 signal peptides in individual experiments to cover both natural signal peptides from multiple organisms as well as synthetic signal peptides.
1. Matthew McCallum et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 373,648-654 (2021).
2. Upadhyay C, et al. Dual Role of HIV-1 Envelope Signal Peptide in Immune Evasion. Viruses. 2022 Apr 13;14(4):808.
3. Upadhyay C, et al. Signal peptide exchange alters HIV-1 envelope antigenicity and immunogenicity. Front Immunol. 2024.
