Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics
Abstract Development of antibodies often begins with the assessment and optimization of their physicochemical properties, and their efficient engagement with the target of interest. Decisions at the early optimization stage are critical for the success of the drug candidate but are constrained due t...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-02-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-87316-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1823862493501456384 |
|---|---|
| author | Krutika Patidar Nikhil Pillai Saroj Dhakal Lindsay B. Avery Panteleimon D. Mavroudis |
| author_facet | Krutika Patidar Nikhil Pillai Saroj Dhakal Lindsay B. Avery Panteleimon D. Mavroudis |
| author_sort | Krutika Patidar |
| collection | DOAJ |
| description | Abstract Development of antibodies often begins with the assessment and optimization of their physicochemical properties, and their efficient engagement with the target of interest. Decisions at the early optimization stage are critical for the success of the drug candidate but are constrained due to the limited knowledge of the antibody and target pharmacology. In the present work, we propose a machine learning-based target pharmacology assessment framework that utilizes minimal physiologically based pharmacokinetic (mPBPK) modeling and machine learning (ML) to infer optimal physicochemical properties of antibodies and their targets. We use a mPBPK model previously developed by our group that incorporates a multivariate quantitative relationship between antibodies’ physicochemical properties such as molecular weight (MW), size, charge, and in silico + in vitro derived descriptors with their PK properties. In this study, we perform a high-throughput exploration of virtual antibody drug candidates with varying physicochemical properties (binding affinity, charge, etc.), and virtual target candidates with varying characteristics (baseline expression, half-life, etc.) to unravel rules for antibody drug candidate selection that achieve favorable drug-target interaction, which is defined by target occupancy (TO) percentage. We identified that variations in the antibody dose and dosing scheme, target form (soluble or membrane-bound), antibody charge, and site of action had a significant effect on the TO and selection criteria for antibody drug candidates. By unraveling new design rules for antibody drug properties that are dependent on ML-based TO assessment, we deliver a first-in-class ML-based target pharmacology assessment framework toward better understanding of the biology-specific PK and ADME processes of antibody drug candidate proteins and reduce the overall time for drug development. |
| format | Article |
| id | doaj-art-87df08a5d0df469b97fc40f1eb5fdb16 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-87df08a5d0df469b97fc40f1eb5fdb162025-02-09T12:31:06ZengNature PortfolioScientific Reports2045-23222025-02-0115111310.1038/s41598-025-87316-wDevelopment of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeuticsKrutika Patidar0Nikhil Pillai1Saroj Dhakal2Lindsay B. Avery3Panteleimon D. Mavroudis4Department of Chemical and Biological Engineering, University at Buffalo, The State University of New YorkGlobal DMPK Modeling & Simulation, SanofiGlobal DMPK Modeling & Simulation, SanofiGlobal DMPK Innovation, SanofiGlobal DMPK Modeling & Simulation, SanofiAbstract Development of antibodies often begins with the assessment and optimization of their physicochemical properties, and their efficient engagement with the target of interest. Decisions at the early optimization stage are critical for the success of the drug candidate but are constrained due to the limited knowledge of the antibody and target pharmacology. In the present work, we propose a machine learning-based target pharmacology assessment framework that utilizes minimal physiologically based pharmacokinetic (mPBPK) modeling and machine learning (ML) to infer optimal physicochemical properties of antibodies and their targets. We use a mPBPK model previously developed by our group that incorporates a multivariate quantitative relationship between antibodies’ physicochemical properties such as molecular weight (MW), size, charge, and in silico + in vitro derived descriptors with their PK properties. In this study, we perform a high-throughput exploration of virtual antibody drug candidates with varying physicochemical properties (binding affinity, charge, etc.), and virtual target candidates with varying characteristics (baseline expression, half-life, etc.) to unravel rules for antibody drug candidate selection that achieve favorable drug-target interaction, which is defined by target occupancy (TO) percentage. We identified that variations in the antibody dose and dosing scheme, target form (soluble or membrane-bound), antibody charge, and site of action had a significant effect on the TO and selection criteria for antibody drug candidates. By unraveling new design rules for antibody drug properties that are dependent on ML-based TO assessment, we deliver a first-in-class ML-based target pharmacology assessment framework toward better understanding of the biology-specific PK and ADME processes of antibody drug candidate proteins and reduce the overall time for drug development.https://doi.org/10.1038/s41598-025-87316-wTarget pharmacology, Antibodies, Pharmacokinetics, High-throughput ML, Decision tree classification. |
| spellingShingle | Krutika Patidar Nikhil Pillai Saroj Dhakal Lindsay B. Avery Panteleimon D. Mavroudis Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics Scientific Reports Target pharmacology, Antibodies, Pharmacokinetics, High-throughput ML, Decision tree classification. |
| title | Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics |
| title_full | Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics |
| title_fullStr | Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics |
| title_full_unstemmed | Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics |
| title_short | Development of an mPBPK machine learning framework for early target pharmacology assessment of biotherapeutics |
| title_sort | development of an mpbpk machine learning framework for early target pharmacology assessment of biotherapeutics |
| topic | Target pharmacology, Antibodies, Pharmacokinetics, High-throughput ML, Decision tree classification. |
| url | https://doi.org/10.1038/s41598-025-87316-w |
| work_keys_str_mv | AT krutikapatidar developmentofanmpbpkmachinelearningframeworkforearlytargetpharmacologyassessmentofbiotherapeutics AT nikhilpillai developmentofanmpbpkmachinelearningframeworkforearlytargetpharmacologyassessmentofbiotherapeutics AT sarojdhakal developmentofanmpbpkmachinelearningframeworkforearlytargetpharmacologyassessmentofbiotherapeutics AT lindsaybavery developmentofanmpbpkmachinelearningframeworkforearlytargetpharmacologyassessmentofbiotherapeutics AT panteleimondmavroudis developmentofanmpbpkmachinelearningframeworkforearlytargetpharmacologyassessmentofbiotherapeutics |