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Record W7132976823

Anionic Acyl Methyl Phosphates for the Synthesis of Hemoglobin-Based Oxygen Therapeutics

2024· dissertation· W7132976823 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueTSpace · 2024
Typedissertation
Language
FieldBiochemistry, Genetics and Molecular Biology
TopicHemoglobin structure and function
Canadian institutionsUniversity of Toronto
Fundersnot available
KeywordsCooperativityReagentOxygenHemoglobinBlood substituteIntramolecular forceMolecule
DOInot available

Abstract

fetched live from OpenAlex

Hemoglobin, contained within red blood cells (RBCs), is the oxygen-carrying unit within humans. Free of the immunogenic problems associated with red blood cells, acellular hemoglobin could be the basis for a universally accepted substitute for the oxygen-carrying function of RBCs. This inspired research on a class of molecules known as hemoglobin-based oxygen carriers (HBOCs) – an area of interest in our research group. Hemoglobin, however, does not function as intended when present outside of RBCs. Decades of research in the field has now established that a viable acellular HBOC must 1) include an intramolecular cross-link to retain function and prevent renal toxicity, 2) be enlarged to prevent adverse cardiovascular effects, notably hypertension, and 3) exhibit cooperativity and physiologically-relevant oxygen affinity. Based on these requirements, our group has developed hemoglobin bis-tetramers – a candidate oxygen carrier utilizing a combination of native protein modifications and bio-orthogonal “click” chemistry. Our method boasts highly selective protein modifications, and thus high homogeneity, in the resulting product. This also makes our method highly reproducible. Other HBOCs in development are often heterogeneous mixtures of compounds, resulting in potentially inconsistent oxygenation properties. The high homogeneity of our method, however, comes at the cost of low synthetic yields. In the present work I utilize anionic acyl phosphate-based reagents to optimize the synthesis of bis-tetramers. My efforts ultimately lead to a three-fold increase in overall yields and significant additional improvements towards scalability. I begin by optimizing the current leading bis-tetramer protocol using an acyl phosphate-based acetylating agent, methyl acetyl phosphate (MAP). Noticing critical shortcomings within this method, I then developed a novel procedure using an acyl phosphate-based azide cross-linker. The cross-linker, PacXL, is the first azide-containing cross-linker to react specifically at the target cross-linking site on hemoglobin. The new protocol also utilizes the R-state conformation of hemoglobin, which is significantly more advantageous towards scale-up compared with the previously used T-state conformation. Outside the context of bis-tetramers, my results also establish acyl phosphates as highly selective reagents for cationic sites and potentiates their broad application towards targeting proteins exhibiting strong cationic character.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow)
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.277
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0010.000
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0010.000
Research integrity0.0010.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.016
GPT teacher head0.318
Teacher spread0.302 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it