Quantum chemical calculations predict biological function: the case of T cell receptor interaction with a peptide/MHC class I

System-agnostic prediction of pharmaceutical excipient miscibility via computing-as-a-service and experimental validation

We applied computing-as-a-service to the unattended system-agnostic miscibility prediction of the pharmaceutical surfactants, Vitamin E TPGS and Tween 80, with Copovidone VA64 polymer at temperature relevant for the pharmaceutical hot melt extrusion process. The computations were performed in lieu of running exhaustive hot melt extrusion experiments to identify surfactant-polymer miscibility limits. The computing scheme involved a massively parallelized architecture for molecular dynamics and free energy perturbation from which binodal, spinodal, and mechanical mixture critical points were detected on molar Gibbs free energy profiles at 180 °C. We established tight agreement between the computed stability (miscibility) limits of 9.0 and 10.0 wt% vs. the experimental 7 and 9 wt% for the Vitamin E TPGS and Tween 80 systems, respectively, and identified different destabilizing mechanisms applicable to each system. This paradigm supports that computational stability prediction may serve as a physically meaningful, resource-efficient, and operationally sensible digital twin to experimental screening tests of pharmaceutical systems. This approach is also relevant to amorphous solid dispersion drug delivery systems, as it can identify critical stability points of active pharmaceutical ingredient/excipient mixtures.

Quantum vaccinomics platforms to advance in vaccinology

The opinion flows from Introduction to the immunological quantum that requires a historical perspective, to Quantum vaccine algorithms supported by a bibliometric analysis, to Quantum vaccinomics describing from our perspective the different vaccinomics and quantum vaccinomics algorithms. Finally, in the Discussion and conclusions we propose novel platforms and algorithms developed to further advance on quantum vaccinomics. In the paper we refer to protective epitopes or immunological quantum for the design of candidate vaccine antigens, which may elicit a protective response through both cellular and antibody mediated mechanisms of the host immune system. Vaccines are key interventions for the prevention and control of infectious diseases affecting humans and animals worldwide. Biophysics led to quantum biology and quantum immunology reflecting quantum dynamics within living systems and their evolution. In analogy to quantum of light, immune protective epitopes were proposed as the immunological quantum. Multiple quantum vaccine algorithms were developed based on omics and other technologies. Quantum vaccinomics is the methodological approach with different platforms used for the identification and combination of immunological quantum for vaccine development. Current quantum vaccinomics platforms include in vitro, in music and in silico algorithms and top trends in biotechnology for the identification, characterization and combination of candidate protective epitopes. These platforms have been applied to different infectious diseases and in the future should target prevalent and emerging infectious diseases with novel algorithms.

A Chirality-Based Quantum Leap

There is increasing interest in the study of chiral degrees of freedom occurring in matter and in electromagnetic fields. Opportunities in quantum sciences will likely exploit two main areas that are the focus of this Review: (1) recent observations of the chiral-induced spin selectivity (CISS) effect in chiral molecules and engineered nanomaterials and (2) rapidly evolving nanophotonic strategies designed to amplify chiral light-matter interactions. On the one hand, the CISS effect underpins the observation that charge transport through nanoscopic chiral structures favors a particular electronic spin orientation, resulting in large room-temperature spin polarizations. Observations of the CISS effect suggest opportunities for spin control and for the design and fabrication of room-temperature quantum devices from the bottom up, with atomic-scale precision and molecular modularity. On the other hand, chiral-optical effects that depend on both spin- and orbital-angular momentum of photons could offer key advantages in all-optical and quantum information technologies. In particular, amplification of these chiral light-matter interactions using rationally designed plasmonic and dielectric nanomaterials provide approaches to manipulate light intensity, polarization, and phase in confined nanoscale geometries. Any technology that relies on optimal charge transport, or optical control and readout, including quantum devices for logic, sensing, and storage, may benefit from chiral quantum properties. These properties can be theoretically and experimentally investigated from a quantum information perspective, which has not yet been fully developed. There are uncharted implications for the quantum sciences once chiral couplings can be engineered to control the storage, transduction, and manipulation of quantum information. This forward-looking Review provides a survey of the experimental and theoretical fundamentals of chiral-influenced quantum effects and presents a vision for their possible future roles in enabling room-temperature quantum technologies.

A Quantum Vaccinomics Approach Based on Protein-Protein Interactions

Vaccines are the most effective preventive intervention to reduce the impact of infectious diseases worldwide. In particular, tick-borne diseases represent a growing burden for human and animal health worldwide and vaccines are the most effective and environmentally sound approach for the control of vector infestations and pathogen transmission. However, the development of effective vaccines for the control of tick-borne diseases with combined vector-derived and pathogen-derived antigens is one of the limitations for the development of effective vaccine formulations. Quantum biology arise from findings suggesting that living cells operate under non-trivial features of quantum mechanics, which has been proposed to be involved in DNA mutation biological process. Then, the electronic structure of the molecular interactions behind peptide immunogenicity led to quantum immunology and based on the definition of the photon as a quantum of light, the immune protective epitopes were proposed as the immunological quantum. Recently, a quantum vaccinomics approach was proposed based on the characterization of the immunological quantum to further advance the design of more effective and safe vaccines. In this chapter, we describe methods of the quantum vaccinomics approach based on proteins with key functions in cell interactome and regulome of vector-host-pathogen interactions for the identification by yeast two-hybrid screen and the characterization by in vitro protein-protein interactions and musical scores of protein interacting domains, and the characterization of conserved protective epitopes in protein interacting domains. These results can then be used for the design and production of chimeric protective antigens.

Vaccinomics: a future avenue for vaccine development against emerging pathogens

INTRODUCTION

Vaccines are a major achievement in medical sciences, but the development of more effective vaccines against infectious diseases is essential for prevention and control of emerging pathogens worldwide. The application of omics technologies has advanced vaccinology through the characterization of host-vector-pathogen molecular interactions and the identification of candidate protective antigens. However, major challenges such as host immunity, pathogen and environmental factors, vaccine efficacy and safety need to be addressed. Vaccinomics provides a platform to address these challenges and improve vaccine efficacy and safety.

AREAS COVERED

In this review, we summarize current information on vaccinomics and propose quantum vaccinomics approaches to further advance vaccine development through the identification and combination of antigen protective epitopes, the immunological quantum. The COVID-19 pandemic caused by SARS-CoV-2 is an example of emerging infectious diseases with global impact on human health.

EXPERT OPINION

Vaccines are required for the effective and environmentally sustainable intervention for the control of emerging infectious diseases worldwide. Recent advances in vaccinomics provide a platform to address challenges in improving vaccine efficacy and implementation. As proposed here, quantum vaccinomics will contribute to vaccine development, efficacy, and safety by facilitating antigen combinations to target pathogen infection and transmission in emerging infectious diseases.

Human Cytomegalovirus variant peptides adapt by decreasing their total coordination upon binding to a T cell receptor

The tertiary structure of the native Cytomegalovirus peptide (NLV) presented by HLA-A2 and bound to the RA14 T cell receptor was used as a reference for the calculation of atomic coordination differences of both the NLV as well as of a number of singly substituted NLV variants in the absence of TCR. Among the pMHC complexes, the native peptide was found to exhibit the highest total coordination difference in respect to the reference structure, suggesting that it experienced the widest structural adaptation upon recognition by the TCR. In addition, the peptide on the isolated NLV-MHC complex was over-coordinated as compared to the rest of the variants. Moreover, the trend was found to account for a set of measured dissociation constants and critical concentrations for target-cell lysis for all variants in complexation with RA14: functionally, all variant peptides were established to be either weak agonists or null peptides, while, at the same time, our current study established that they were also under-coordinated in respect to NLV. It could, thus, be argued that the most ‘efficient’ structural adaptation upon pMHC recognition by the TCR requires of the peptide to undergo the widest under-coordination possible. The main structural characteristic which differentiated the NLV in respect to the variants was a the presence of 16 oxygen atoms (waters) in the former׳s second coordination shell which accounted for over-coordination of roughly 100% and 30% in the O–O and C–O partials respectively. In fact, in the absence of second shell oxygens, the NLV peptide was decidedly under-coordinated in respect to all of the variants, as also suggested by the C–C partial.

Atomic Coordination Reflects Peptide Immunogenicity

We demonstrated that the immunological identity of variant peptides may be accurately predicted on the basis of atomic coordination of both unprotonated and protonated tertiary structures, provided that the structure of the native peptide (index) is known. The metric which was discovered to account for this discrimination is the coordination difference between the variant and the index; we also showed that increasing coordination difference in respect to the index was correlated to a correspondingly weakening immunological outcome of the variant. Additionally, we established that this metric quickly seizes to operate beyond the peptide scale, e.g., within a coordination shell inclusive of atoms up to a distance of 7 Å away from the peptide or over the entire pMHC-TCR complex. Analysis of molecular orbital interactions for a range of formal charges further revealed that the N-terminus of the agonists was always able to sustain a stable ammonium (NH3+) group which was consistently absent in antagonists. We deem that the presence of NH3+ constitutes a secondary observable with a biological consequence, signifying a change in T cell activation. While our analysis of protonated structures relied on the quantum chemical relaxation of the H species, the results were consistent across a wide range of peptide charge and spin polarization conditions.

The coordination of unprotonated peptide tertiary structure as a metric of pMHC-TCR functional avidity

The coordination difference between the unprotonated tertiary structures of a native (Tax) peptide and a number of its variants – all peptides presented by HLA-A201 and bound to the human A6 T cell receptor-was discovered to constitute a metric of pMHC–TCR functional avidity. Moreover, increasing coordination deviations from the index were found to flag correspondingly weakening immunological outcomes of the variant peptides. The prognostic utility of the coordination difference of unprotonated tertiary structure was established to operate strictly on the peptide scale, seizing to be of relevance either to the immediate peptide environment (i.e. within the realm of peptide short range order, within 7 Å of any peptide atom) or over the entirety of the pMHC–TCR complex. Additionally, the imprint of peptide immunological identity was expressed both by the total coordination as well as by its C–C partial.