1
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Bendtsen KM, Harder MWH, Glendorf T, Kjeldsen TB, Kristensen NR, Refsgaard HHF. Predicting human half-life for insulin analogs: An inter-drug approach. Eur J Pharm Biopharm 2024; 201:114375. [PMID: 38897553 DOI: 10.1016/j.ejpb.2024.114375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
An inter-drug approach, applying pharmacokinetic information for insulin analogs in different animal species, rat, dog and pig, performed better compared to allometric scaling for human translation of intra-venous half-life and only required data from a single animal species for reliable predictions. Average fold error (AFE) between 1.2-1.7 were determined for all species and for multispecies allometric scaling AFE was 1.9. A slightly larger prediction error for human half-life was determined from in vitro human insulin receptor affinity data (AFE on 2.3-2.6). The requirements for the inter-drug approach were shown to be a span of at least 2 orders of magnitude in half-life for the included drugs and a shared clearance mechanism. The insulin analogs in this study were the five fatty acid protracted analogs: Insulin degludec, insulin icodec, insulin 320, insulin 338 and insulin 362, as well as the non-acylated analog insulin aspart.
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Affiliation(s)
- Kristian M Bendtsen
- Digital Sciences & Innovation, Research & Early Development, Novo Nordisk, DK-2760 Måløv, Denmark
| | - Magnus W H Harder
- Global Drug Discovery, Research & Early Development, Novo Nordisk, DK-2760 Måløv, Denmark
| | - Tine Glendorf
- Global Research Technologies, Research & Early Development, Novo Nordisk, DK-2760 Måløv, Denmark
| | - Thomas B Kjeldsen
- Global Research Technologies, Research & Early Development, Novo Nordisk, DK-2760 Måløv, Denmark
| | | | - Hanne H F Refsgaard
- Global Drug Discovery, Research & Early Development, Novo Nordisk, DK-2760 Måløv, Denmark.
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2
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Bryniarski MA, Tuhin MTH, Acker TM, Wakefield DL, Sethaputra G, Cook KD, Soto M, Ponce M, Primack R, Jagarapu A, LaGory EL, Conner KP. Cellular neonatal Fc receptor recycling efficiencies can differentiate target-independent clearance mechanisms of monoclonal antibodies. J Pharm Sci 2024:S0022-3549(24)00235-1. [PMID: 38906252 DOI: 10.1016/j.xphs.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
In vivo clearance mechanisms of therapeutic monoclonal antibodies (mAbs) encompass both target-mediated and target-independent processes. Two distinct determinants of overall mAb clearance largely separate of target-mediated influences are non-specific cellular endocytosis and subsequent pH-dependent mAb recycling mediated by the neonatal Fc receptor (FcRn), where inter-mAb variability in the efficiency of both processes is observed. Here, we implemented a functional cell-based FcRn recycling assay via Madin-Darby canine kidney type II cells stably co-transfected with human FcRn and its light chain β2-microglobulin. A series of pH-dependent internalization studies using a model antibody demonstrated proper function of the human FcRn complex. We then applied our cellular assays to assess the contribution of FcRn and non-specific interactions in the cellular turnover for a panel of 8 clinically relevant mAbs exhibiting variable human pharmacokinetic behavior. Our results demonstrate that non-specific endocytosis rates, pH-dependent non-specific interactions, and engagement with FcRn all contribute to the overall recycling efficiency of therapeutic monoclonal antibodies. The predictive capacity of our assay approach was highlighted by successful identification of all mAbs within our panel possessing clearance in humans greater than 5 mL/day/kg. These results demonstrate that a combination of cell-based in vitro assays can properly resolve individual mechanisms underlying the overall in vivo recycling efficiency and non-target mediated clearance of therapeutic mAbs.
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Affiliation(s)
- Mark A Bryniarski
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080.
| | - Md Tariqul Haque Tuhin
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Timothy M Acker
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Devin L Wakefield
- Research Biomics, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Gemy Sethaputra
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Kevin D Cook
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Marcus Soto
- Pharmacokinetics & Drug Metabolism, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Manuel Ponce
- Pharmacokinetics & Drug Metabolism, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Ronya Primack
- Pharmacokinetics & Drug Metabolism, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Aditya Jagarapu
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Edward L LaGory
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080
| | - Kip P Conner
- Pharmacokinetics and Drug Metabolism, Amgen Research, 750 Gateway Blvd, Suite 100, South San Francisco, CA 94080.
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3
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Cook KD, Tran T, Thomas VA, Devanaboyina SC, Rock DA, Pearson JT. Correlation of In Vitro Kinetic Stability to Preclinical In Vivo Pharmacokinetics for a Panel of Anti-PD-1 Monoclonal Antibody Interleukin 21 Mutein Immunocytokines. Drug Metab Dispos 2024; 52:228-235. [PMID: 38135505 DOI: 10.1124/dmd.123.001555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023] Open
Abstract
The development of therapeutic fusion protein drugs is often impeded by the unintended consequences that occur from fusing together domains from independent naturally occurring proteins, consequences such as altered biodistribution, tissue uptake, or rapid clearance and potential immunogenicity. For therapeutic fusion proteins containing globular domains, we hypothesized that aberrant in vivo behavior could be related to low kinetic stability of these domains leading to local unfolding and susceptibility to partial proteolysis and/or salvage and uptake. Herein we describe an assay to measure kinetic stability of therapeutic fusion proteins by way of their sensitivity to the protease thermolysin. The results indicate that in vivo pharmacokinetics of a panel of anti-programmed cell death protein 1 monocolonal antibody:interleukin 21 immunocytokines in both mice and nonhuman primates are highly correlated with their in vitro susceptibility to thermolysin-mediated proteolysis. This assay can be used as a tool to quickly identify in vivo liabilities of globular domains of therapeutic proteins, thus aiding in the optimization and development of new multispecific drug candidates. SIGNIFICANCE STATEMENT: This work describes a novel assay utilizing protein kinetic stability to identify preclinical in vivo pharmacokinetic liabilities of multispecific therapeutic fusion proteins. This provides an efficient, inexpensive method to ascertain inherent protein stability in vitro before conducting in vivo studies, which can rapidly increase the speed of preclinical drug development.
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Affiliation(s)
- Kevin D Cook
- Amgen Research, Pharmacokinetics & Drug Metabolism, South San Francisco, California
| | - Thuy Tran
- Amgen Research, Pharmacokinetics & Drug Metabolism, South San Francisco, California
| | - Veena A Thomas
- Amgen Research, Pharmacokinetics & Drug Metabolism, South San Francisco, California
| | | | - Dan A Rock
- Amgen Research, Pharmacokinetics & Drug Metabolism, South San Francisco, California
| | - Josh T Pearson
- Amgen Research, Pharmacokinetics & Drug Metabolism, South San Francisco, California
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4
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Nielsen GH, Schmitz ZD, Hackel BJ. Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization. Protein Eng Des Sel 2024; 37:gzae010. [PMID: 38836499 PMCID: PMC11170491 DOI: 10.1093/protein/gzae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/06/2024] Open
Abstract
Protein developability is requisite for use in therapeutic, diagnostic, or industrial applications. Many developability assays are low throughput, which limits their utility to the later stages of protein discovery and evolution. Recent approaches enable experimental or computational assessment of many more variants, yet the breadth of applicability across protein families and developability metrics is uncertain. Here, three library-scale assays-on-yeast protease, split green fluorescent protein (GFP), and non-specific binding-were evaluated for their ability to predict two key developability outcomes (thermal stability and recombinant expression) for the small protein scaffolds affibody and fibronectin. The assays' predictive capabilities were assessed via both linear correlation and machine learning models trained on the library-scale assay data. The on-yeast protease assay is highly predictive of thermal stability for both scaffolds, and the split-GFP assay is informative of affibody thermal stability and expression. The library-scale data was used to map sequence-developability landscapes for affibody and fibronectin binding paratopes, which guides future design of variants and libraries.
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Affiliation(s)
- Gregory H Nielsen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Zachary D Schmitz
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
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5
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Park E, Izadi S. Molecular surface descriptors to predict antibody developability: sensitivity to parameters, structure models, and conformational sampling. MAbs 2024; 16:2362788. [PMID: 38853585 PMCID: PMC11168226 DOI: 10.1080/19420862.2024.2362788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
In silico assessment of antibody developability during early lead candidate selection and optimization is of paramount importance, offering a rapid and material-free screening approach. However, the predictive power and reproducibility of such methods depend heavily on the selection of molecular descriptors, model parameters, accuracy of predicted structure models, and conformational sampling techniques. Here, we present a set of molecular surface descriptors specifically designed for predicting antibody developability. We assess the performance of these descriptors by benchmarking their correlations with an extensive array of experimentally determined biophysical properties, including viscosity, aggregation, hydrophobic interaction chromatography, human pharmacokinetic clearance, heparin retention time, and polyspecificity. Further, we investigate the sensitivity of these surface descriptors to methodological nuances, such as the choice of interior dielectric constant, hydrophobicity scales, structure prediction methods, and the impact of conformational sampling. Notably, we observe systematic shifts in the distribution of surface descriptors depending on the structure prediction method used, driving weak correlations of surface descriptors across structure models. Averaging the descriptor values over conformational distributions from molecular dynamics mitigates the systematic shifts and improves the consistency across different structure prediction methods, albeit with inconsistent improvements in correlations with biophysical data. Based on our benchmarking analysis, we propose six in silico developability risk flags and assess their effectiveness in predicting potential developability issues for a set of case study molecules.
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Affiliation(s)
- Eliott Park
- Pharmaceutical Development, Genentech Inc, South San Francisco, CA, USA
| | - Saeed Izadi
- Pharmaceutical Development, Genentech Inc, South San Francisco, CA, USA
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6
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Aertker KM, Pilvankar MR, Prass TM, Blech M, Higel F, Kasturirangan S. Exploring molecular determinants and pharmacokinetic properties of IgG1-scFv bispecific antibodies. MAbs 2024; 16:2318817. [PMID: 38444390 PMCID: PMC10936634 DOI: 10.1080/19420862.2024.2318817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Bispecific antibodies (BsAbs) capable of recognizing two distinct epitopes or antigens offer promising therapeutic options for various diseases by targeting multiple pathways. The favorable pharmacokinetic (PK) properties of monoclonal antibodies (mAbs) are crucial, as they directly influence patient safety and therapeutic efficacy. For numerous mAb therapeutics, optimization of neonatal Fc receptor (FcRn) interactions and elimination of unfavorable molecular properties have led to improved PK properties. However, many BsAbs exhibit unfavorable PK, which has precluded their development as drugs. In this report, we present studies on the molecular determinants underlying the distinct PK profiles of three IgG1-scFv BsAbs. Our study indicated that high levels of nonspecific interactions, elevated isoelectric point (pI), and increased number of positively charged patches contributed to the fast clearance of IgG1-scFv. FcRn chromatography results revealed specific scFv-FcRn interactions that are unique to the IgG1-scFv, which was further supported by molecular dynamics (MD) simulation. These interactions likely stabilize the BsAb FcRn interaction at physiological pH, which in turn could disrupt FcRn-mediated BsAb recycling. In addition to the empirical observations, we also evaluated the impact of in silico properties, including pI differential between the Fab and scFv and the ratio of dipole moment to hydrophobic moment (RM) and their correlation with the observed clearance. These findings highlight that the PK properties of BsAbs may be governed by novel determinants, owing to their increased structural complexity compared to immunoglobulin G (IgG) 1 antibodies.
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Affiliation(s)
- Kristina M.J. Aertker
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | - Tobias M. Prass
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany
| | - Michaela Blech
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Fabian Higel
- Global CMC Experts NBE, Global Quality Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Srinath Kasturirangan
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
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7
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Makowski EK, Wang T, Zupancic JM, Huang J, Wu L, Schardt JS, De Groot AS, Elkins SL, Martin WD, Tessier PM. Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning. Nat Biomed Eng 2024; 8:45-56. [PMID: 37666923 PMCID: PMC10842909 DOI: 10.1038/s41551-023-01074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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8
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Arras P, Yoo HB, Pekar L, Clarke T, Friedrich L, Schröter C, Schanz J, Tonillo J, Siegmund V, Doerner A, Krah S, Guarnera E, Zielonka S, Evers A. AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study. Front Mol Biosci 2023; 10:1249247. [PMID: 37842638 PMCID: PMC10575757 DOI: 10.3389/fmolb.2023.1249247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and nextgeneration sequencing (NGS) in combination with artificial intelligence and machine learning methods (AI/ML) for the identification of de novo humanized single domain antibodies (sdAbs) with favorable early developability profiles. Methods: The display library was derived from a novel approach, in which VHH-based CDR3 regions obtained from a llama (Lama glama), immunized against NKp46, were grafted onto a humanized VHH backbone library that was diversified in CDR1 and CDR2. Following NGS analysis of sequence pools from two rounds of fluorescence-activated cell sorting we focused on four sequence clusters based on NGS frequency and enrichment analysis as well as in silico developability assessment. For each cluster, long short-term memory (LSTM) based deep generative models were trained and used for the in silico sampling of new sequences. Sequences were subjected to sequence- and structure-based in silico developability assessment to select a set of less than 10 sequences per cluster for production. Results: As demonstrated by binding kinetics and early developability assessment, this procedure represents a general strategy for the rapid and efficient design of potent and automatically humanized sdAb hits from screening selections with favorable early developability profiles.
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Affiliation(s)
- Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Thomas Clarke
- Bioinformatics, EMD Serono, Billerica, MA, United States
| | - Lukas Friedrich
- Computational Chemistry and Biologics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Jennifer Schanz
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Jason Tonillo
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Enrico Guarnera
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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9
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Einarson K, Bendtsen KM, Li K, Thomsen M, Kristensen NR, Winther O, Fulle S, Clemmensen L, Refsgaard HH. Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs. ACS OMEGA 2023; 8:23566-23578. [PMID: 37426277 PMCID: PMC10324072 DOI: 10.1021/acsomega.3c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023]
Abstract
Therapeutic peptides and proteins derived from either endogenous hormones, such as insulin, or de novo design via display technologies occupy a distinct pharmaceutical space in between small molecules and large proteins such as antibodies. Optimizing the pharmacokinetic (PK) profile of drug candidates is of high importance when it comes to prioritizing lead candidates, and machine-learning models can provide a relevant tool to accelerate the drug design process. Predicting PK parameters of proteins remains difficult due to the complex factors that influence PK properties; furthermore, the data sets are small compared to the variety of compounds in the protein space. This study describes a novel combination of molecular descriptors for proteins such as insulin analogs, where many contained chemical modifications, e.g., attached small molecules for protraction of the half-life. The underlying data set consisted of 640 structural diverse insulin analogs, of which around half had attached small molecules. Other analogs were conjugated to peptides, amino acid extensions, or fragment crystallizable regions. The PK parameters clearance (CL), half-life (T1/2), and mean residence time (MRT) could be predicted by using classical machine-learning models such as Random Forest (RF) and Artificial Neural Networks (ANN) with root-mean-square errors of CL of 0.60 and 0.68 (log units) and average fold errors of 2.5 and 2.9 for RF and ANN, respectively. Both random and temporal data splittings were employed to evaluate ideal and prospective model performance with the best models, regardless of data splitting, achieving a minimum of 70% of predictions within a twofold error. The tested molecular representations include (1) global physiochemical descriptors combined with descriptors encoding the amino acid composition of the insulin analogs, (2) physiochemical descriptors of the attached small molecule, (3) protein language model (evolutionary scale modeling) embedding of the amino acid sequence of the molecules, and (4) a natural language processing inspired embedding (mol2vec) of the attached small molecule. Encoding the attached small molecule via (2) or (4) significantly improved the predictions, while the benefit of using the protein language model-based encoding (3) depended on the used machine-learning model. The most important molecular descriptors were identified as descriptors related to the molecular size of both the protein and protraction part using Shapley additive explanations values. Overall, the results show that combining representations of proteins and small molecules was key for PK predictions of insulin analogs.
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Affiliation(s)
- Kasper
A. Einarson
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
- Novo
Nordisk A/S, Global Drug Discovery, Research
& Early Development (R&ED), Måløv 2760, Denmark
| | | | - Kang Li
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | - Maria Thomsen
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | | | - Ole Winther
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
- Center
for Genomic Medicine, Rigshospitalet (Copenhagen
University Hospital), Copenhagen 2100, Denmark
- Department
of Biology, Bioinformatics Centre, University
of Copenhagen, Copenhagen 2200, Denmark
| | - Simone Fulle
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | - Line Clemmensen
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
| | - Hanne H.F. Refsgaard
- Novo
Nordisk A/S, Global Drug Discovery, Research
& Early Development (R&ED), Måløv 2760, Denmark
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10
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El-Atawneh S, Goldblum A. Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes. J Chem Inf Model 2023. [PMID: 37257045 DOI: 10.1021/acs.jcim.2c01531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
G protein-coupled receptors (GPCRs) are targets of many drugs, of which ∼25% are indicated for central nervous system (CNS) disorders. Drug promiscuity affects their efficacy and safety profiles. Predicting the polypharmacology profile of compounds against GPCRs can thus provide a basis for producing more precise therapeutics by considering the targets and the anti-targets in that family of closely related proteins. We provide a tool for predicting the polypharmacology of compounds within prominent GPCR families in the CNS: serotonin, dopamine, histamine, muscarinic, opioid, and cannabinoid receptors. Our in-house algorithm, "iterative stochastic elimination" (ISE), produces high-quality ligand-based models for agonism and antagonism at 31 GPCRs. The ISE models correctly predict 68% of CNS drug-GPCR interactions, while the "similarity ensemble approach" predicts only 33%. The activity models correctly predict 56% of reported activities of DrugBank molecules for these CNS receptors. We conclude that the combination of interactions and activity profiles generated by screening through our models form the basis for subsequent designing and discovering novel therapeutics, either single, multitargeting, or repurposed.
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Affiliation(s)
- Shayma El-Atawneh
- Molecular Modelling and Drug Design Lab, Institute for Drug Research and Fraunhofer Project Center for Drug Discovery and Delivery, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Amiram Goldblum
- Molecular Modelling and Drug Design Lab, Institute for Drug Research and Fraunhofer Project Center for Drug Discovery and Delivery, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
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11
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Liu S, Shah DK. Physiologically Based Pharmacokinetic Modeling to Characterize the Effect of Molecular Charge on Whole-Body Disposition of Monoclonal Antibodies. AAPS J 2023; 25:48. [PMID: 37118220 DOI: 10.1208/s12248-023-00812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023] Open
Abstract
Motivated by a series of work demonstrating the effect of molecular charge on antibody pharmacokinetics (PK), physiological-based pharmacokinetic (PBPK) models are emerging that relate in silico calculated charge or in vitro measures of polyspecificity to antibody PK parameters. However, only plasma data has been used for model development in these studies, leading to unvalidated assumptions. Here, we present an extended platform PBPK model for antibodies that incorporate charge-dependent endothelial cell pinocytosis rate and nonspecific off-target binding in the interstitial space and on circulating blood cells, to simultaneously characterize whole-body disposition of three antibody charge variants. Predictive potential of various charge metrics was also explored, and the difference between positive charge patches and negative charge patches (i.e., PPC-PNC) was used as the charge parameter to establish quantitative relationships with nonspecific binding affinities and endothelial cell uptake rate. Whole-body disposition of these charge variants was captured well by the model, with less than 2-fold predictive error in area under the curve of most plasma and tissue PK data. The model also predicted that with greater positive charge, nonspecific binding was more substantial, and pinocytosis rate increased especially in brain, heart, kidney, liver, lung, and spleen, but remained unchanged in adipose, bone, muscle, and skin. The presented PBPK model contributes to our understanding of the mechanisms governing the disposition of charged antibodies and can be used as a platform to guide charge engineering based on desired plasma and tissue exposures.
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Affiliation(s)
- Shufang Liu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, 455 Pharmacy Building, Buffalo, Ney York, 14214-8033, USA
| | - Dhaval K Shah
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, 455 Pharmacy Building, Buffalo, Ney York, 14214-8033, USA.
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12
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Obrezanova O. Artificial intelligence for compound pharmacokinetics prediction. Curr Opin Struct Biol 2023; 79:102546. [PMID: 36804676 DOI: 10.1016/j.sbi.2023.102546] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 02/17/2023]
Abstract
Optimisation of compound pharmacokinetics (PK) is an integral part of drug discovery and development. Animal in vivo PK data as well as human and animal in vitro systems are routinely utilised to evaluate PK in humans. In recent years machine learning and artificial intelligence (AI) emerged as a major tool for modelling of in vivo animal and human PK, enabling prediction from chemical structure early in drug discovery, and therefore offering opportunities to guide the design and prioritisation of molecules based on relevant in vivo properties and, ultimately, predicting human PK at the point of design. This review presents recent advances in machine learning and AI models for in vivo animal and human PK for small-molecule compounds as well as some examples for antibody therapeutics.
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Affiliation(s)
- Olga Obrezanova
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, CB4 0WJ, UK.
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13
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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14
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Datta-Mannan A, Molitoris BA, Feng Y, Martinez MM, Sandoval RM, Brown RM, Merkel D, Croy JE, Dunn KW. Intravital Microscopy Reveals Unforeseen Biodistribution Within the Liver and Kidney Mechanistically Connected to the Clearance of a Bifunctional Antibody. Drug Metab Dispos 2023; 51:403-412. [PMID: 36460476 PMCID: PMC11022859 DOI: 10.1124/dmd.122.001049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/16/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Bifunctional antibody (BfAb) therapeutics offer the potential for novel functionalities beyond those of the individual monospecific entities. However, combining these entities into a single molecule can have unpredictable effects, including changes in pharmacokinetics that limit the compound's therapeutic profile. A better understanding of how molecular modifications affect in vivo tissue interactions could help inform BfAb design. The present studies were predicated on the observation that a BfAb designed to have minimal off-target interactions cleared from the circulation twice as fast as the monoclonal antibody (mAb) from which it was derived. The present study leverages the spatial and temporal resolution of intravital microscopy (IVM) to identify cellular interactions that may explain the different pharmacokinetics of the two compounds. Disposition studies of mice demonstrated that radiolabeled compounds distributed similarly over the first 24 hours, except that BfAb accumulated approximately two- to -three times more than mAb in the liver. IVM studies of mice demonstrated that both distributed to endosomes of liver endothelia but with different kinetics. Whereas mAb accumulated rapidly within the first hour of administration, BfAb accumulated only modestly during the first hour but continued to accumulate over 24 hours, ultimately reaching levels similar to those of the mAb. Although neither compound was freely filtered by the mouse or rat kidney, BfAb, but not mAb, was found to accumulate over 24 hours in endosomes of proximal tubule cells. These studies demonstrate how IVM can be used as a tool in drug design, revealing unpredicted cellular interactions that are undetectable by conventional analyses. SIGNIFICANCE STATEMENT: Bifunctional antibodies offer novel therapeutic functionalities beyond those of the individual monospecific entities. However, combining these entities into a single molecule can have unpredictable effects, including undesirable changes in pharmacokinetics. Studies of the dynamic distribution of a bifunctional antibody and its parent monoclonal antibody presented here demonstrate how intravital microscopy can expand our understanding of the in vivo disposition of therapeutics, detecting off-target interactions that could not be detected by conventional pharmacokinetics approaches or predicted by conventional physicochemical analyses.
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Affiliation(s)
- Amita Datta-Mannan
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Bruce A Molitoris
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Yiqing Feng
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Michelle M Martinez
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Ruben M Sandoval
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Robin M Brown
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Daniel Merkel
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Johnny E Croy
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
| | - Kenneth W Dunn
- Exploratory Medicine and Pharmacology (A.D-M.), Clinical Laboratory Services (R.M.B.), and Biotechnology Discovery Research (Y.F., D.M., J.E.C.), Lilly Research Laboratories, Indianapolis, Indiana and Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana (K.W.D.)
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15
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Computational and artificial intelligence-based methods for antibody development. Trends Pharmacol Sci 2023; 44:175-189. [PMID: 36669976 DOI: 10.1016/j.tips.2022.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
Abstract
Due to their high target specificity and binding affinity, therapeutic antibodies are currently the largest class of biotherapeutics. The traditional largely empirical antibody development process is, while mature and robust, cumbersome and has significant limitations. Substantial recent advances in computational and artificial intelligence (AI) technologies are now starting to overcome many of these limitations and are increasingly integrated into development pipelines. Here, we provide an overview of AI methods relevant for antibody development, including databases, computational predictors of antibody properties and structure, and computational antibody design methods with an emphasis on machine learning (ML) models, and the design of complementarity-determining region (CDR) loops, antibody structural components critical for binding.
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16
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Jain T, Boland T, Vásquez M. Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches. MAbs 2023; 15:2200540. [PMID: 37072706 PMCID: PMC10114995 DOI: 10.1080/19420862.2023.2200540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
With the growing significance of antibodies as a therapeutic class, identifying developability risks early during development is of paramount importance. Several high-throughput in vitro assays and in silico approaches have been proposed to de-risk antibodies during early stages of the discovery process. In this review, we have compiled and collectively analyzed published experimental assessments and computational metrics for clinical antibodies. We show that flags assigned based on in vitro measurements of polyspecificity and hydrophobicity are more predictive of clinical progression than their in silico counterparts. Additionally, we assessed the performance of published models for developability predictions on molecules not used during model training. We find that generalization to data outside of those used for training remains a challenge for models. Finally, we highlight the challenges of reproducibility in computed metrics arising from differences in homology modeling, in vitro assessments relying on complex reagents, as well as curation of experimental data often used to assess the utility of high-throughput approaches. We end with a recommendation to enable assay reproducibility by inclusion of controls with disclosed sequences, as well as sharing of structural models to enable the critical assessment and improvement of in silico predictions.
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Affiliation(s)
| | - Todd Boland
- Computational Biology, Adimab LLC, Lebanon, NH, USA
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17
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Evers A, Malhotra S, Bolick WG, Najafian A, Borisovska M, Warszawski S, Fomekong Nanfack Y, Kuhn D, Rippmann F, Crespo A, Sood V. SUMO: In Silico Sequence Assessment Using Multiple Optimization Parameters. Methods Mol Biol 2023; 2681:383-398. [PMID: 37405660 DOI: 10.1007/978-1-0716-3279-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
To select the most promising screening hits from antibody and VHH display campaigns for subsequent in-depth profiling and optimization, it is highly desirable to assess and select sequences on properties beyond only their binding signals from the sorting process. In addition, developability risk criteria, sequence diversity, and the anticipated complexity for sequence optimization are relevant attributes for hit selection and optimization. Here, we describe an approach for the in silico developability assessment of antibody and VHH sequences. This method not only allows for ranking and filtering multiple sequences with regard to their predicted developability properties and diversity, but also visualizes relevant sequence and structural features of potentially problematic regions and thereby provides rationales and starting points for multi-parameter sequence optimization.
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Affiliation(s)
- Andreas Evers
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany.
| | - Shipra Malhotra
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | - Ahmad Najafian
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Maria Borisovska
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | | | - Daniel Kuhn
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Friedrich Rippmann
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Alejandro Crespo
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Vanita Sood
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
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18
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Mock M, Jacobitz AW, Langmead CJ, Sudom A, Yoo D, Humphreys SC, Alday M, Alekseychyk L, Angell N, Bi V, Catterall H, Chen CC, Chou HT, Conner KP, Cook KD, Correia AR, Dykstra A, Ghimire-Rijal S, Graham K, Grandsard P, Huh J, Hui JO, Jain M, Jann V, Jia L, Johnstone S, Khanal N, Kolvenbach C, Narhi L, Padaki R, Pelegri-O'Day EM, Qi W, Razinkov V, Rice AJ, Smith R, Spahr C, Stevens J, Sun Y, Thomas VA, van Driesche S, Vernon R, Wagner V, Walker KW, Wei Y, Winters D, Yang M, Campuzano IDG. Development of in silico models to predict viscosity and mouse clearance using a comprehensive analytical data set collected on 83 scaffold-consistent monoclonal antibodies. MAbs 2023; 15:2256745. [PMID: 37698932 PMCID: PMC10498806 DOI: 10.1080/19420862.2023.2256745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/16/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Biologic drug discovery pipelines are designed to deliver protein therapeutics that have exquisite functional potency and selectivity while also manifesting biophysical characteristics suitable for manufacturing, storage, and convenient administration to patients. The ability to use computational methods to predict biophysical properties from protein sequence, potentially in combination with high throughput assays, could decrease timelines and increase the success rates for therapeutic developability engineering by eliminating lengthy and expensive cycles of recombinant protein production and testing. To support development of high-quality predictive models for antibody developability, we designed a sequence-diverse panel of 83 effector functionless IgG1 antibodies displaying a range of biophysical properties, produced and formulated each protein under standard platform conditions, and collected a comprehensive package of analytical data, including in vitro assays and in vivo mouse pharmacokinetics. We used this robust training data set to build machine learning classifier models that can predict complex protein behavior from these data and features derived from predicted and/or experimental structures. Our models predict with 87% accuracy whether viscosity at 150 mg/mL is above or below a threshold of 15 centipoise (cP) and with 75% accuracy whether the area under the plasma drug concentration-time curve (AUC0-672 h) in normal mouse is above or below a threshold of 3.9 × 106 h x ng/mL.
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Affiliation(s)
- Marissa Mock
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Alex W Jacobitz
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Athena Sudom
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Daniel Yoo
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Sara C Humphreys
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Mai Alday
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | | | - Nicolas Angell
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Vivian Bi
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Hannah Catterall
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Chen-Chun Chen
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Hui-Ting Chou
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Kip P Conner
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Kevin D Cook
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Ana R Correia
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Andrew Dykstra
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Kevin Graham
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Peter Grandsard
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Joon Huh
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - John O Hui
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Mani Jain
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Victoria Jann
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Lei Jia
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Sheree Johnstone
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Neelam Khanal
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Carl Kolvenbach
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Linda Narhi
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Rupa Padaki
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Wei Qi
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Austin J Rice
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Richard Smith
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Christopher Spahr
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | | | - Yax Sun
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Veena A Thomas
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | | | - Robert Vernon
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Victoria Wagner
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Kenneth W Walker
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Yangjie Wei
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Dwight Winters
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Melissa Yang
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
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19
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Liu S, Humphreys SC, Cook KD, Conner KP, Correia AR, Jacobitz AW, Yang M, Primack R, Soto M, Padaki R, Lubomirski M, Smith R, Mock M, Thomas VA. Utility of physiologically based pharmacokinetic modeling to predict inter-antibody variability in monoclonal antibody pharmacokinetics in mice. MAbs 2023; 15:2263926. [PMID: 37824334 PMCID: PMC10572049 DOI: 10.1080/19420862.2023.2263926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023] Open
Abstract
In this investigation, we tested the hypothesis that a physiologically based pharmacokinetic (PBPK) model incorporating measured in vitro metrics of off-target binding can largely explain the inter-antibody variability in monoclonal antibody (mAb) pharmacokinetics (PK). A diverse panel of 83 mAbs was evaluated for PK in wild-type mice and subjected to 10 in vitro assays to measure major physiochemical attributes. After excluding for target-mediated elimination and immunogenicity, 56 of the remaining mAbs with an eight-fold variability in the area under the curve (A U C 0 - 672 h : 1.74 × 106 -1.38 × 107 ng∙h/mL) and 10-fold difference in clearance (2.55-26.4 mL/day/kg) formed the training set for this investigation. Using a PBPK framework, mAb-dependent coefficients F1 and F2 modulating pinocytosis rate and convective transport, respectively, were estimated for each mAb with mostly good precision (coefficient of variation (CV%) <30%). F1 was estimated to be the mean and standard deviation of 0.961 ± 0.593, and F2 was estimated to be 2.13 ± 2.62. Using principal component analysis to correlate the regressed values of F1/F2 versus the multidimensional dataset composed of our panel of in vitro assays, we found that heparin chromatography retention time emerged as the predictive covariate to the mAb-specific F1, whereas F2 variability cannot be well explained by these assays. A sigmoidal relationship between F1 and the identified covariate was incorporated within the PBPK framework. A sensitivity analysis suggested plasma concentrations to be most sensitive to F1 when F1 > 1. The predictive utility of the developed PBPK model was evaluated against a separate panel of 14 mAbs biased toward high clearance, among which area under the curve of PK data of 12 mAbs was predicted within 2.5-fold error, and the positive and negative predictive values for clearance prediction were 85% and 100%, respectively. MAb heparin chromatography assay output allowed a priori identification of mAb candidates with unfavorable PK.
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Affiliation(s)
- Shufang Liu
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Sara C. Humphreys
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Kevin D. Cook
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Kip P. Conner
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | | | | | - Melissa Yang
- Therapeutic Discovery, Amgen, Thousand Oaks, CA, USA
| | - Ronya Primack
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, Thousand Oaks, CA, USA
| | - Marcus Soto
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, Thousand Oaks, CA, USA
| | - Rupa Padaki
- Process Development, Amgen Inc, Thousand Oaks, CA, USA
| | | | - Richard Smith
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Marissa Mock
- Therapeutic Discovery, Amgen, Thousand Oaks, CA, USA
| | - Veena A. Thomas
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
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20
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Hu S, Datta-Mannan A, D'Argenio DZ. Monoclonal Antibody Pharmacokinetics in Cynomolgus Monkeys Following Subcutaneous Administration: Physiologically Based Model Predictions from Physiochemical Properties. AAPS J 2022; 25:5. [PMID: 36456779 DOI: 10.1208/s12248-022-00772-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
An integrated physiologically based modeling framework is presented for predicting pharmacokinetics and bioavailability of subcutaneously administered monoclonal antibodies in cynomolgus monkeys, based on in silico structure-derived metrics characterizing antibody size, overall charge, local charge, and hydrophobicity. The model accounts for antibody-specific differences in pinocytosis, transcapillary transport, local lymphatic uptake, and pre-systemic degradation at the subcutaneous injection site and reliably predicts the pharmacokinetics of five different wild-type mAbs and their Fc variants following intravenous and subcutaneous administration. Significant associations were found between subcutaneous injection site degradation rate and the antibody's local positive charge of its complementarity-determining region (R = 0.56, p = 0.0012), antibody pinocytosis rate and its overall positive charge (R = 0.59, p = 0.00063), and antibody paracellular transport and its overall charge together with hydrophobicity (R = 0.63, p = 0.00096). Based on these results, population simulations were performed to predict the relationship between bioavailability and antibody local positive charge. In addition, model simulations were conducted to calculate the relative contribution of absorption pathways (lymphatic and blood), pre-systemic degradation pathways (interstitial and lysosomal), and the influence of injection site lymph flow on antibody bioavailability and pharmacokinetics. The proposed physiologically based modeling framework integrates fundamental mechanisms governing antibody subcutaneous absorption and disposition, with structured-based physiochemical properties, to predict antibody bioavailability and pharmacokinetics in vivo.
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Affiliation(s)
- Shihao Hu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, 90089, USA
| | - Amita Datta-Mannan
- Department of Exploratory Medicine and Pharmacology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - David Z D'Argenio
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, 90089, USA.
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21
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Ball K, Bruin G, Escandon E, Funk C, Pereira JN, Yang TY, Yu H. Characterizing the pharmacokinetics and biodistribution of therapeutic proteins: an industry white paper. Drug Metab Dispos 2022; 50:858-866. [PMID: 35149542 DOI: 10.1124/dmd.121.000463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 01/06/2022] [Indexed: 11/22/2022] Open
Abstract
Characterization of the pharmacokinetics (PK) and biodistribution of therapeutic proteins (TPs) is a hot topic within the pharmaceutical industry, particularly with an ever-increasing catalog of novel modality TPs. Here, we review the current practices, and provide a summary of extensive cross-company discussions as well as a survey completed by International Consortium for Innovation and Quality (IQ consortium) members on this theme. A wide variety of in vitro, in vivo and in silico techniques are currently used to assess PK and biodistribution of TPs, and we discuss the relevance of these from an industry perspective, focusing on PK/PD understanding at the preclinical stage of development, and translation to human. We consider that the 'traditional in vivo biodistribution study' is becoming insufficient as a standalone tool, and thorough characterization of the interaction of the TP with its target(s), target biology, and off-target interactions at a microscopic scale are key to understand the overall biodistribution at a full-body scale. Our summary of the current challenges and our recommendations to address these issues could provide insight into the implementation of best practices in this area of drug development, and continued cross-company collaboration will be of tremendous value. Significance Statement The Innovation & Quality Consortium (IQ) Translational and ADME Sciences Leadership Group (TALG) working group for the ADME of therapeutic proteins evaluates the current practices, recent advances, and challenges in characterizing the PK and biodistribution of therapeutic proteins during drug development, and proposes recommendations to address these issues. Incorporating the in vitro, in vivo and in silico approaches discussed herein may provide a pragmatic framework to increase early understanding of PK/PD relationships, and aid translational modelling for first-in-human dose predictions.
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Affiliation(s)
| | - Gerard Bruin
- Novartis Institutes for Biomedical Research, Switzerland
| | | | - Christoph Funk
- Dept. of Drug Metabolism and Pharmacokinetics, F. Hoffmann-La Roche Ltd., Switzerland
| | | | | | - Hongbin Yu
- Boehringer Ingelheim Pharmaceuticals, Inc, United States
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22
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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23
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Hu S, Datta-Mannan A, D’Argenio DZ. Physiologically Based Modeling to Predict Monoclonal Antibody Pharmacokinetics in Humans from in vitro Physiochemical Properties. MAbs 2022; 14:2056944. [PMID: 35491902 PMCID: PMC9067474 DOI: 10.1080/19420862.2022.2056944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/01/2022] Open
Abstract
A model-based framework is presented to predict monoclonal antibody (mAb) pharmacokinetics (PK) in humans based on in vitro measures of antibody physiochemical properties. A physiologically based pharmacokinetic (PBPK) model is used to explore the predictive potential of 14 in vitro assays designed to measure various antibody physiochemical properties, including nonspecific cell-surface interactions, FcRn binding, thermal stability, hydrophobicity, and self-association. Based on the mean plasma PK time course data of 22 mAbs from humans reported in the literature, we found a significant positive correlation (R = 0.64, p = .0013) between the model parameter representing antibody-specific vascular to endothelial clearance and heparin relative retention time, an in vitro measure of nonspecific binding. We also found that antibody-specific differences in paracellular transport due to convection and diffusion could be partially explained by antibody heparin relative retention time (R = 0.52, p = .012). Other physiochemical properties, including antibody thermal stability, hydrophobicity, cross-interaction and self-association, in and of themselves were not predictive of model-based transport parameters. In contrast to other studies that have reported empirically derived expressions relating in vitro measures of antibody physiochemical properties directly to antibody clearance, the proposed PBPK model-based approach for predicting mAb PK incorporates fundamental mechanisms governing antibody transport and processing, informed by in vitro measures of antibody physiochemical properties, and can be expanded to include more descriptive representations of each of the antibody processing subsystems, as well as other antibody-specific information.
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Affiliation(s)
- Shihao Hu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Amita Datta-Mannan
- Department of Exploratory Medicine and Pharmacology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - David Z. D’Argenio
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
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24
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Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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25
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Negron C, Fang J, McPherson MJ, Stine WB, McCluskey AJ. Separating clinical antibodies from repertoire antibodies, a path to in silico developability assessment. MAbs 2022; 14:2080628. [PMID: 35771588 PMCID: PMC9255221 DOI: 10.1080/19420862.2022.2080628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Approaches for antibody discovery have seen substantial improvement and success in recent years. Yet, advancing antibodies into the clinic remains difficult because therapeutic developability concerns are challenging to predict. We developed a computational model to simplify antibody developability assessment and enable accelerated early-stage screening. To this end, we quantified the ability of hundreds of sequence- and structure-based descriptors to differentiate clinical antibodies that have undergone rigorous screening and characterization for drug-like properties from antibodies in the human repertoire that are not natively paired. This analysis identified 144 descriptors capable of distinguishing clinical from repertoire antibodies. Five descriptors were selected and combined based on performance and orthogonality into a single model referred to as the Therapeutic Antibody Developability Analysis (TA-DA). On a hold-out test set, this tool separated clinical antibodies from repertoire antibodies with an AUC = 0.8, demonstrating the ability to identify developability attributes unique to clinical antibodies. Based on our results, the TA-DA score may serve as an approach for selecting lead antibodies for further development. Abbreviations: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy (AC-SINS), Area Under the Curve (AUC), Complementary-Determining Region (CDR), Clinical-Stage Therapeutics (CST), Framework (FR), Monoclonal Antibodies (mAbs), Observed Antibody Space (OAS), Receiver Operating Characteristic (ROC), Size-Exclusion Chromatography (SEC), Structural Aggregation Propensity (SAP), Therapeutic Antibody Developability Analysis (TA-DA), Therapeutic Antibody Profiler (TAP), Therapeutic Structural Antibody Database (Thera-SAbDab), Variable Heavy (VH), Variable Light (VL).
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Affiliation(s)
| | - Joyce Fang
- AbbVie Bioresearch Center, Worcester, MA, USA
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26
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Pharmacokinetic Developability and Disposition Profiles of Bispecific Antibodies: A Case Study with Two Molecules. Antibodies (Basel) 2021; 11:antib11010002. [PMID: 35076469 PMCID: PMC8788489 DOI: 10.3390/antib11010002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Bispecific antibodies (BsAb) that engage multiple pathways are a promising therapeutic strategy to improve and prolong the efficacy of biologics in complex diseases. In the early stages of discovery, BsAbs often exhibit a broad range of pharmacokinetic (PK) behavior. Optimization of the neonatal Fc receptor (FcRn) interactions and removal of undesirable physiochemical properties have been used to improve the 'pharmacokinetic developability' for various monoclonal antibody (mAb) therapeutics, yet there is a sparsity of such information for BsAbs. The present work evaluated the influence of FcRn interactions and inherent physiochemical properties on the PK of two related single chain variable fragment (scFv)-based BsAbs. Despite their close relation, the two BsAbs exhibit disparate PK in cynomolgus monkeys with BsAb-1 having an aberrant clearance of ~2 mL/h/kg and BsAb-2 displaying a an ~10-fold slower clearance (~0.2 mL/h/kg). Evaluation of the physiochemical characteristics of the molecules, including charge, non-specific binding, thermal stability, and hydrophobic properties, as well as FcRn interactions showed some differences. In-depth drug disposition results revealed that a substantial disparity in the complete release from FcRn at a neutral pH is a primary factor contributing to the rapid clearance of the BsAb-1 while other biophysical characteristics were largely comparable between molecules.
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27
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Thorsteinson N, Gunn JR, Kelly K, Long W, Labute P. Structure-based charge calculations for predicting isoelectric point, viscosity, clearance, and profiling antibody therapeutics. MAbs 2021; 13:1981805. [PMID: 34632944 PMCID: PMC8510563 DOI: 10.1080/19420862.2021.1981805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The effect of hydrophobicity on antibody aggregation is well understood, and it has been shown that charge calculations can be useful for high-concentration viscosity and pharmacokinetic (PK) clearance predictions. In this work, structure-based charge descriptors are evaluated for their predictive performance on recently published antibody pI, viscosity, and clearance data. From this, we devised four rules for therapeutic antibody profiling which address developability issues arising from hydrophobicity and charged-based solution behavior, PK, and the ability to enrich for those that are approved by the U.S. Food and Drug Administration. Differences in strategy for optimizing the solution behavior of human IgG1 antibodies versus the IgG2 and IgG4 isotypes and the impact of pH alterations in formulation are discussed.
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Affiliation(s)
- Nels Thorsteinson
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - John R Gunn
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Kenneth Kelly
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Will Long
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Paul Labute
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
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