Periodic Reporting for period 4 - DeNovoImmunoDesign (Computational Design of Novel Functional Proteins for Immunoengineering)
Reporting period: 2021-09-01 to 2022-12-31
Our ERC starting grant entitled “DeNovoImmunoDesign: Computational design of novel functional proteins for Immunoengineering” addresses two main challenges: I) How can we rationally design proteins to perform novel functions using computational approaches? II) Can we use these computationally designed proteins in the broad area of Immunoengineering to develop better vaccines and cancer immunotherapies?
Proteins are important molecular components that are ubiquitous to all cellular functions underlying normal and disease states of organisms. Despite the many years of research and the large body of work that has been performed by the scientific community – to engineer proteins with predictable stabilities and functional activities remains a very difficult task. Mostly, these challenges arise due to the large amino-acid sequence space available to design these molecules and also due to our poor understanding of the physical and chemical principles that govern protein structure and function.
To tackle such a fundamental problem in biology and bioengineering in our project we proposed to develop novel computational methods to aid the process of designing new functional proteins. Within the scope of our project these newly designed proteins will be used to create novel proteins that can be used as vaccines against viral pathogens (Respiratory Syncytial Virus, Influenza) and in another application such proteins can be used embedded in cellular therapies used in cancer immunotherapy to provide safety mechanisms that can make these treatments safer.
In a broader context our work has societal impact through the development of protein engineering tools that can be used to create novel molecular agents with impact in human health, specifically:
I) Protein-based drugs (e.g. antibodies) are the fastest growing segment of clinically approved drugs – an improved understanding and design of this broad class of molecules will certainly lead to better molecules with impact for human health and biotechnology
II) As proof-of-concept for the design of novel protein -based drugs we have computationally designed and experimentally characterized protein that bind an neutralize SARS-COV2 and engage efficiently immuno-checkpoint receptors that can be important for immunotherapy
III) Novel vaccine antigens for next-generation vaccines – vaccines are one of the most safe and efficacious therapeutic interventions in modern medicine. However, due to the capabilities of the pathogens to evade to the immune system novel vaccine concepts are needed. Our project proposes some solutions for this problem.
IV) Together with protein-based drugs an important area for human health is that of cell-based therapies. Cell-based therapies have the potential to act as living drugs and integrate external signals to adapt their output. One of the first examples of cell based therapies are chimeric antigenic receptor (CAR) T-cells which are currently an approved treatment for lymphoma. Cell-based therapies carry an enormous potential but also important risks. Within the scope of this project we also engineered novel protein-protein interactions that could be used to control the activity of CAR-T cells.
Proteins are important molecular components that are ubiquitous to all cellular functions underlying normal and disease states of organisms. Despite the many years of research and the large body of work that has been performed by the scientific community – to engineer proteins with predictable stabilities and functional activities remains a very difficult task. Mostly, these challenges arise due to the large amino-acid sequence space available to design these molecules and also due to our poor understanding of the physical and chemical principles that govern protein structure and function.
To tackle such a fundamental problem in biology and bioengineering in our project we proposed to develop novel computational methods to aid the process of designing new functional proteins. Within the scope of our project these newly designed proteins will be used to create novel proteins that can be used as vaccines against viral pathogens (Respiratory Syncytial Virus, Influenza) and in another application such proteins can be used embedded in cellular therapies used in cancer immunotherapy to provide safety mechanisms that can make these treatments safer.
In a broader context our work has societal impact through the development of protein engineering tools that can be used to create novel molecular agents with impact in human health, specifically:
I) Protein-based drugs (e.g. antibodies) are the fastest growing segment of clinically approved drugs – an improved understanding and design of this broad class of molecules will certainly lead to better molecules with impact for human health and biotechnology
II) As proof-of-concept for the design of novel protein -based drugs we have computationally designed and experimentally characterized protein that bind an neutralize SARS-COV2 and engage efficiently immuno-checkpoint receptors that can be important for immunotherapy
III) Novel vaccine antigens for next-generation vaccines – vaccines are one of the most safe and efficacious therapeutic interventions in modern medicine. However, due to the capabilities of the pathogens to evade to the immune system novel vaccine concepts are needed. Our project proposes some solutions for this problem.
IV) Together with protein-based drugs an important area for human health is that of cell-based therapies. Cell-based therapies have the potential to act as living drugs and integrate external signals to adapt their output. One of the first examples of cell based therapies are chimeric antigenic receptor (CAR) T-cells which are currently an approved treatment for lymphoma. Cell-based therapies carry an enormous potential but also important risks. Within the scope of this project we also engineered novel protein-protein interactions that could be used to control the activity of CAR-T cells.
Main results achieved:
I) The development of a protein design method (Topobuilder) which has been made publicly available and was used to engineer synthetic immunogens against the Respiratory Syncytial Virus.
II) For the first time, a cocktail of synthetic immunogens elicited neutralization antibodies consistently within an animal cohort- an essential requirement for any vaccine
III) We created novel protein components which the assembly is sensitive to the activity of clinically approved drugs – we then showed that such protein components can be used to control the activity of CAR-T cell therapies.
IV) A methodology for the design of novel protein-protein interactions that can be used to create molecules with therapeutic potential such as protein-based inhibitors
I) The development of a protein design method (Topobuilder) which has been made publicly available and was used to engineer synthetic immunogens against the Respiratory Syncytial Virus.
II) For the first time, a cocktail of synthetic immunogens elicited neutralization antibodies consistently within an animal cohort- an essential requirement for any vaccine
III) We created novel protein components which the assembly is sensitive to the activity of clinically approved drugs – we then showed that such protein components can be used to control the activity of CAR-T cell therapies.
IV) A methodology for the design of novel protein-protein interactions that can be used to create molecules with therapeutic potential such as protein-based inhibitors
I) We used machine learning techniques to analyze protein surfaces in a novel way and identify imprinted patterns that allow us to predict accurately, important functional characteristics of proteins. We foresee that until the end of the project we will be able to demonstrate that these technologies will have an important impact in the way that we can design novel proteins with biological function – particularly on the field of de novo protein interactions. This computer program was named MaSIF.
II) For the first time we showed that our protein surface description can be used for efficient molecular design of novel proteins for an extremely challenging task as the design of novel protein protein interactions.
III) In parallel with the aforementioned methodological approaches we are also developing a computational protein design approach which is focused in mimic functional protein surfaces. This methodological approach will broaden the design possibilities to create synthetic immunogens that mimic structurally complex epitopes that were out of reach of the other methodologies developed in this project. We foresee its usage in pathogens like Influenza and Dengue where the complexity of the relevant epitope will preclude the utilization of other more simplistic methods.
IIIV) We have currently several generations of synthetic immunogens that are being formulated in cocktail vaccines against RSV. Our latest results indicate that these epitope-focused vaccines are able to elicit targeted responses against multiple neutralization epitopes in our RSV model pathogen. In the next stages we will evaluate this capability applied to other pathogens of interest such as Influenza.
II) For the first time we showed that our protein surface description can be used for efficient molecular design of novel proteins for an extremely challenging task as the design of novel protein protein interactions.
III) In parallel with the aforementioned methodological approaches we are also developing a computational protein design approach which is focused in mimic functional protein surfaces. This methodological approach will broaden the design possibilities to create synthetic immunogens that mimic structurally complex epitopes that were out of reach of the other methodologies developed in this project. We foresee its usage in pathogens like Influenza and Dengue where the complexity of the relevant epitope will preclude the utilization of other more simplistic methods.
IIIV) We have currently several generations of synthetic immunogens that are being formulated in cocktail vaccines against RSV. Our latest results indicate that these epitope-focused vaccines are able to elicit targeted responses against multiple neutralization epitopes in our RSV model pathogen. In the next stages we will evaluate this capability applied to other pathogens of interest such as Influenza.