In Silico Assessment of Biomolecule Reactivity with Leachables

References

1. 1.↵
   1. Markovic I.

   Evaluation of Safety and Quality Impact of Extractable and Leachable Substances in Therapeutic Biologic Protein Products: A Risk-Based Perspective. Expert Opin. Drug Saf. 2007, 6 (5), 487–491.

   OpenUrlCrossRefPubMedWeb of Science
2. 2.↵
   U.S. Food and Drug Administration, Guidance for Industry: Container Closure Systems for Packaging Human Drugs and Biologics. Chemistry, Manufacturing, and Controls Documentation. Center for Biologics Evaluation and Research. U.S. Department of Health and Human Services: Rockville, MD, 1999.
3. 3.↵
   Product Quality Research Institute. Safety Thresholds and Best Demonstrated Practices for Extractables and Leachables in Parenteral Drug Products (Intravenous, Subcutaneous, and Intramuscular). PQRI, 2021.
4. 4.↵
   1. Dobo K. L.,
   2. Greene N.,
   3. Fred C.,
   4. Glowienke S.,
   5. Harvey J. S.,
   6. Hasselgren C.,
   7. Jolly R.,
   8. Kenyon M. O.,
   9. Munzner J. B.,
   10. Muster W.,
   11. Neft R.,
   12. Vijayaraj Reddy M.,
   13. White A. T.,
   14. Weiner S.

   In Silico Methods Combined with Expert Knowledge Rule out Mutagenic Potential of Pharmaceutical Impurities: An Industry Survey. Regul. Toxicol. Pharmacol. 2012, 62 (3), 449–455.

   OpenUrlCrossRefPubMed
5. 5.↵
   1. Bercu J.,
   2. Masuda‐Herrera M. J.,
   3. Trejo-Martin A.,
   4. Hasselgren C.,
   5. Lord J.,
   6. Graham J.,
   7. Schmitz M.,
   8. Milchak L.,
   9. Owens C.,
   10. Lal S. H.,
   11. Robinson R. M.,
   12. Whalley S.,
   13. Bellion P.,
   14. Vuorinen A.,
   15. Gromek K.,
   16. Hawkins W. A.,
   17. van de Gevel I.,
   18. Vriens K.,
   19. Kemper R.,
   20. Naven R.,
   21. Ferrer P.,
   22. Myatt G. J.

   A Cross-Industry Collaboration to Assess If Acute Oral Toxicity (Q)SAR Models Are Fit-for-Purpose for GHS Classification and Labelling. Regul. Toxicol. Pharmacol. 2021, 120, 104843

   OpenUrl
6. 6.↵
   1. Schwöbel J. A. H.,
   2. Koleva Y. K.,
   3. Enoch S. J.,
   4. Bajot F.,
   5. Hewitt M.,
   6. Madden J. C.,
   7. Roberts D. W.,
   8. Schultz T. W.,
   9. Cronin M. T. D.

   Measurement and Estimation of Electrophilic Reactivity for Predictive Toxicology. Chem. Rev. 2011, 111 (4), 2562–2596.

   OpenUrlCrossRefPubMedWeb of Science
7. 7.↵
   1. Pearson R. G.

   Hard and Soft Acids and Bases—The Evolution of a Chemical Concept. Coord. Chem. Rev 1990, 100, 403–425.

   OpenUrlCrossRef
8. 8.↵
   1. LoPachin R. M.,
   2. Geohagen B. C.,
   3. Nordstroem L. U.

   Mechanisms of Soft and Hard Electrophile Toxicities. Toxicology 2019, 418, 62–69.

   OpenUrl
9. 9.↵
   1. Myatt G. J.,
   2. Ahlberg E.,
   3. Akahori Y.,
   4. Allen D.,
   5. Amberg A.,
   6. Anger L. T.,
   7. Aptula A.,
   8. Auerbach S.,
   9. Beilke L.,
   10. Bellion P.,
   11. Benigni R.,
   12. Bercu J.,
   13. Booth E. D.,
   14. Bower D.,
   15. Brigo A.,
   16. Burden N.,
   17. Cammerer Z.,
   18. Cronin M. T. D.,
   19. Cross K. P.,
   20. Custer L.,
   21. Dettwiler M.,
   22. Dobo K.,
   23. Ford K. A.,
   24. Fortin M. C.,
   25. Gad-McDonald S. E.,
   26. Gellatly N.,
   27. Gervais V.,
   28. Glover K. P.,
   29. Glowienke S.,
   30. Van Gompel J.,
   31. Gutsell S.,
   32. Hardy B.,
   33. Harvey J. S.,
   34. Hillegass J.,
   35. Honma M.,
   36. Hsieh J.-H.,
   37. Hsu C.-W.,
   38. Hughes K.,
   39. Johnson C.,
   40. Jolly R.,
   41. Jones D.,
   42. Kemper R.,
   43. Kenyon M. O.,
   44. Kim M. T.,
   45. Kruhlak N. L.,
   46. Kulkarni S. A.,
   47. Kümmerer K.,
   48. Leavitt P.,
   49. Majer B.,
   50. Masten S.,
   51. Miller S.,
   52. Moser J.,
   53. Mumtaz M.,
   54. Muster W.,
   55. Neilson L.,
   56. Oprea T. I.,
   57. Patlewicz G.,
   58. Paulino A.,
   59. Lo Piparo E.,
   60. Powley M.,
   61. Quigley D. P.,
   62. Reddy M. V.,
   63. Richarz A.-N.,
   64. Ruiz P.,
   65. Schilter B.,
   66. Serafimova R.,
   67. Simpson W.,
   68. Stavitskaya L.,
   69. Stidl R.,
   70. Suarez-Rodriguez D.,
   71. Szabo D. T.,
   72. Teasdale A.,
   73. Trejo-Martin A.,
   74. Valentin J.-P.,
   75. Vuorinen A.,
   76. Wall B. A.,
   77. Watts P.,
   78. White A. T.,
   79. Wichard J.,
   80. Witt K. L.,
   81. Woolley A.,
   82. Woolley D.,
   83. Zwickl C.,
   84. Hasselgren C.

   In Silico Toxicology Protocols. Regul. Toxicol. Pharmacol. 2018, 96, 1–17.

   OpenUrl
10. 10.↵
    International Conference for Harmonisation, ICH M7(R1): Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals to Limit Potential Carcinogenic Risk. ICH: Geneva, 2017.
11. 11.↵
    1. Amberg A.,
    2. Beilke L.,
    3. Bercu J.,
    4. Bower D.,
    5. Brigo A.,
    6. Cross K. P.,
    7. Custer L.,
    8. Dobo K.,
    9. Dowdy E.,
    10. Ford K. A.,
    11. Glowienke S.,
    12. Van Gompel J.,
    13. Harvey J.,
    14. Hasselgren C.,
    15. Honma M.,
    16. Jolly R.,
    17. Kemper R.,
    18. Kenyon M.,
    19. Kruhlak N.,
    20. Leavitt P.,
    21. Miller S.,
    22. Muster W.,
    23. Nicolette J.,
    24. Plaper A.,
    25. Powley M.,
    26. Quigley D. P.,
    27. Reddy M. V.,
    28. Spirkl H.-P.,
    29. Stavitskaya L.,
    30. Teasdale A.,
    31. Weiner S.,
    32. Welch D. S.,
    33. White A.,
    34. Wichard J.,
    35. Myatt G. J.

    Principles and Procedures for Implementation of ICH M7 Recommended (Q)SAR Analyses. Regul. Toxicol. Pharmacol. 2016, 77, 13–24.

    OpenUrl
12. 12.↵
    OECD. Guidance Document on the Validation of (Quantitative) Structure-Activity Relationship [(Q)Sar] Models. OECD Publishing: Paris, 2007.
13. 13.↵
    1. Aptula A. O.,
    2. Patlewicz G.,
    3. Roberts D. W.

    Skin Sensitization: Reaction Mechanistic Applicability Domains for Structure-Activity Relationships. Chem. Res. Toxicol. 2005, 18 (9), 1420–1426.

    OpenUrlCrossRefPubMedWeb of Science
14. 14.↵
    1. Aptula A. O.,
    2. Roberts D. W.

    Mechanistic Applicability Domains for Nonanimal-Based Prediction of Toxicological End Points: General Principles and Application to Reactive Toxicity. Chem. Res. Toxicol. 2006, 19 (8), 1097–1105.

    OpenUrlCrossRefPubMedWeb of Science
15. 15.↵
    1. Nelms M. D.,
    2. Cronin M. T. D.,
    3. Schultz T. W.,
    4. Enoch S. J.

    Experimental Verification, and Domain Definition, of Structural Alerts for Protein Binding: Epoxides, Lactones, Nitroso, Nitros, Aldehydes and Ketones. SAR QSAR Environ. Res. 2013, 24 (9), 695–709.

    OpenUrl
16. 16.↵
    1. Wijeyesakere S. J.,
    2. Wilson D. M.,
    3. Settivari R.,
    4. Auernhammer T. R.,
    5. Parks A. K.,
    6. Marty M. S.

    Development of a Profiler for Facile Chemical Reactivity Using the Open-Source Konstanz Information Miner. Appl. In Vitro Toxicol. 2018, 4 (2).
17. 17.↵
    Leadscope. Instem Computational Toxicology. 2022.
18. 18.↵
    OECD. Test No. 442C: In Chemico Skin Sensitisation: Assays Addressing the Adverse Outcome Pathway Key Event on Covalent Binding to Proteins; OECD Guidelines for the Testing of Chemicals, Section 4; OECD Publishing: Paris, 2019. doi:10.1787/9789264229709-en.

    OpenUrlCrossRef
19. 19.↵
    1. Miller E. C.,
    2. Miller J. A.

    Searches for Ultimate Chemical Carcinogens and Their Reactions with Cellular Macromolecules. Cancer 1981, 47 (10), 2327–2345.

    OpenUrlCrossRefPubMedWeb of Science
20. 20.↵
    1. DeMarini D.

    The Role of Genotoxicity in Carcinogenesis. In Tumour Site Concordance and Mechanisms of Carcinogenesis; IARC Scientific Publications, No. 165; International Agency for Research on Cancer: Lyon, France, 2019; Chapter 12.
21. 21.↵
    1. Williams G. M.

    DNA Reactive and Epigenetic Carcinogens. Exp. Toxicol. Pathol. 1992, 44 (8), 457–463.

    OpenUrlPubMedWeb of Science
22. 22.↵
    1. Benigni R.,
    2. Bossa C.

    Mechanisms of Chemical Carcinogenicity and Mutagenicity: A Review with Implications for Predictive Toxicology. Chem. Rev. 2011, 111 (4), 2507–2536.

    OpenUrlCrossRefPubMedWeb of Science
23. 23.↵
    1. Benigni R.,
    2. Bossa C.,
    3. Tcheremenskaia O.

    Nongenotoxic Carcinogenicity of Chemicals: Mechanisms of Action and Early Recognition through a New Set of Structural Alerts. Chem. Rev. 2013, 113 (5), 2940–2957.

    OpenUrlCrossRefPubMedWeb of Science
24. 24.↵
    1. Bailey A. B.,
    2. Chanderbhan R.,
    3. Collazo-Braier N.,
    4. Cheeseman M. A.,
    5. Twaroski M. L.

    The Use of Structure–Activity Relationship Analysis in the Food Contact Notification Program. Regul. Toxicol. Pharmacol. 2005, 42 (2), 225–235.

    OpenUrlCrossRefPubMedWeb of Science
25. 25.↵
    1. Enoch S. J.,
    2. Cronin M. T. D.

    A Review of the Electrophilic Reaction Chemistry Involved in Covalent DNA Binding. Crit. Rev. Toxicol. 2010, 40 (8), 728–748.

    OpenUrlPubMed
26. 26.↵
    1. Kazius J.,
    2. McGuire R.,
    3. Bursi R.

    Derivation and Validation of Toxicophores for Mutagenicity Prediction. J. Med. Chem. 2005, 48 (1), 312–320.

    OpenUrlCrossRefPubMedWeb of Science
27. 27.↵
    1. Enoch S. J.,
    2. Cronin M. T. D.

    Development of New Structural Alerts Suitable for Chemical Category Formation for Assigning Covalent and Non-Covalent Mechanisms Relevant to DNA Binding. Mutat. Res. 2012, 743 (1–2), 10–19.

    OpenUrlPubMed
28. 28.↵
    1. Shamovsky I.,
    2. Ripa L.,
    3. Blomberg N.,
    4. Eriksson L. A.,
    5. Hansen P.,
    6. Mee C.,
    7. Tyrchan C.,
    8. O'Donovan M.,
    9. Sjö P.

    Theoretical Studies of Chemical Reactivity of Metabolically Activated Forms of Aromatic Amines toward DNA. Chem. Res. Toxicol. 2012, 25 (10), 2236–2252.

    OpenUrlPubMed
29. 29.↵
    1. Roemer E.,
    2. Meisgen T.,
    3. Diekmann J.,
    4. Conroy L.,
    5. Stabbert R.

    Heterocyclic Aromatic Amines and Their Contribution to the Bacterial Mutagenicity of the Particulate Phase of Cigarette Smoke. Toxicol. Lett. 2016, 243, 40–47.

    OpenUrl
30. 30.↵
    1. Felton J. S.,
    2. Knize M. G.,
    3. Dolbeare F. A.,
    4. Wu R.

    Mutagenic Activity of Heterocyclic Amines in Cooked Foods. Environ. Health Perspect. 1994, 102 (Suppl. 6), 201–204.

    OpenUrl
31. 31.↵
    1. Robbana-Barnat S.,
    2. Rabache M.,
    3. Rialland E.,
    4. Fradin J.

    Heterocyclic Amines: Occurrence and Prevention in Cooked Food. Environ. Health Perspect. 1996, 104 (3), 280–288.

    OpenUrlPubMedWeb of Science
32. 32.↵
    1. Gao Y.,
    2. Allison N.

    Extractables and Leachables Issues with the Application of Single Use Technology in the Biopharmaceutical Industry. J. Chem. Technol. Biotechnol. 2016, 91 (2), 289–295.

    OpenUrl
33. 33.↵
    1. Broschard T. H.,
    2. Glowienke S.,
    3. Bruen U. S.,
    4. Nagao L. M.,
    5. Teasdale A.,
    6. Stults C. L. M.,
    7. Li K. L.,
    8. Iciek L. A.,
    9. Erexson G.,
    10. Martin E. A.,
    11. Ball D. J.

    Assessing Safety of Extractables from Materials and Leachables in Pharmaceuticals and Biologics—Current Challenges and Approaches. Regul. Toxicol. Pharmacol. 2016, 81, 201–211.

    OpenUrl
34. 34.↵
    1. Monza E.,
    2. Gil V.,
    3. Lucas M. F.

    Computational Enzyme Design at Zymvol. Methods Mol. Biol. 2022, 2397, 249–259.

    OpenUrl
35. 35.↵
    EPA. CompTox Chemicals Dashboard. https://comptox.epa.gov/dashboard/chemical-lists/ELSIE. (accessed December 10, 2021).
36. 36.↵
    1. Isaacs K. K.,
    2. Goldsmith M.-R.,
    3. Egeghy P.,
    4. Phillips K.,
    5. Brooks R.,
    6. Hong T.,
    7. Wambaugh J. F.

    Characterization and Prediction of Chemical Functions and Weight Fractions in Consumer Products. Toxicol. Rep. 2016, 3, 723–732.

    OpenUrl
37. 37.↵
    1. Kroes R.,
    2. Renwick A. G.,
    3. Cheeseman M.,
    4. Kleiner J.,
    5. Mangelsdorf I.,
    6. Piersma A.,
    7. Schilter B.,
    8. Schlatter J.,
    9. van Schothorst F.,
    10. Vos J. G.,
    11. Würtzen G.

    Structure-Based Thresholds of Toxicological Concern (TTC): Guidance for Application to Substances Present at Low Levels in the Diet. Food Chem. Toxicol. 2004, 42 (1), 65–83.

    OpenUrlCrossRefPubMedWeb of Science
38. 38.↵
    Nelson Labs. https://www.nelsonlabs.com/
39. 39.↵
    1. Johnson C.,
    2. Anger L. T.,
    3. Benigni R.,
    4. Bower D.,
    5. Bringezu F.,
    6. Crofton K. M.,
    7. Cronin M. T. D.,
    8. Cross K. P.,
    9. Dettwiler M.,
    10. Frericks M.,
    11. Melnikov F.,
    12. Miller S.,
    13. Roberts D. W.,
    14. Suarez-Rodrigez D.,
    15. Roncaglioni A.,
    16. Lo Piparo E.,
    17. Tice R. R.,
    18. Zwickl C.,
    19. Myatt G. J.

    Evaluating Confidence in Toxicity Assessments Based on Experimental Data and In Silico Predictions. Comput. Toxicol. 2022, 21, 100204

    OpenUrl
40. 40.↵
    1. Honma M.,
    2. Kitazawa A.,
    3. Cayley A.,
    4. Williams R. V.,
    5. Barber C.,
    6. Hanser T.,
    7. Saiakhov R.,
    8. Chakravarti S.,
    9. Myatt G. J.,
    10. Cross K. P.,
    11. Benfenati E.,
    12. Raitano G.,
    13. Mekenyan O.,
    14. Petkov P.,
    15. Bossa C.,
    16. Benigni R.,
    17. Battistelli C. L.,
    18. Giuliani A.,
    19. Tcheremenskaia O.,
    20. DeMeo C.,
    21. Norinder U.,
    22. Koga H.,
    23. Jose C.,
    24. Jeliazkova N.,
    25. Kochev N.,
    26. Paskaleva V.,
    27. Yang C.,
    28. Daga P. R.,
    29. Clark R. D.,
    30. Rathman J.

    Improvement of Quantitative Structure–Activity Relationship (QSAR) Tools for Predicting Ames Mutagenicity: Outcomes of the Ames/QSAR International Challenge Project. Mutagenesis 2018, 34 (1), 3–16.

    OpenUrl
41. 41.↵
    1. Stavitskaya L.,
    2. Minnier B. L.,
    3. Kruhlak N. L.

    Benchmarking Assessment of Open Source and Newly Released Salmonella Mutagenicity (Q)SAR Models for Potential Use Under ICH M7. Presented at SOT 2014, Abstract # 2273b.
42. 42.↵
    1. Natsch A.,
    2. Ryan C. A.,
    3. Foertsch L.,
    4. Emter R.,
    5. Jaworska J.,
    6. Gerberick F.,
    7. Kern P.

    A Dataset on 145 Chemicals Tested in Alternative Assays for Skin Sensitization Undergoing Prevalidation. J. Appl. Toxicol. 2013, 33 (11), 1337–1352.

    OpenUrlPubMed
43. 43.↵
    1. Li K.,
    2. Rogers G.,
    3. Nashed-Samuel Y.,
    4. Lee H.,
    5. Mire-Sluis A.,
    6. Cherney B.,
    7. Forster R.,
    8. Yeh P.,
    9. Markovic I.

    Creating a Holistic Extractables and Leachables (E&L) Program for Biotechnology Products. PDA J. Pharm. Sci. Technol. 2015, 69 (5), 590–619.

    OpenUrlAbstract/FREE Full Text
44. 44.↵
    1. Roberts D. W.,
    2. Aptula A. O.,
    3. Patlewicz G.

    Mechanistic Applicability Domains for Non-Animal Based Prediction of Toxicological Endpoints. QSAR Analysis of the Schiff Base Applicability Domain for Skin Sensitization. Chem. Res. Toxicol. 2006, 19 (9), 1228–1233.

    OpenUrlCrossRefPubMedWeb of Science
45. 45.↵
    1. Kannan V.,
    2. Narayanaswamy P.,
    3. Gadamsetty D.,
    4. Hazra P.,
    5. Khedkar A.,
    6. Iyer H.

    A Tandem Mass Spectrometric Approach to the Identification of O-Glycosylated Glargine Glycoforms in Active Pharmaceutical Ingredient Expressed in Pichia pastoris. Rapid Commun. Mass Spectrom. 2009, 23 (7), 1035–1042.

    OpenUrlCrossRefPubMed
46. 46.↵
    1. Stopfer L. E.,
    2. D'Souza A. D.,
    3. White F. M.

    1,2,3, MHC: A Review of Mass-Spectrometry-Based Immunopeptidomics Methods for Relative and Absolute Quantification of pMHCs. Immuno-Oncology Technol. 2021, 11, 100042

    OpenUrl
47. 47.↵
    1. Metz B.,
    2. Kersten G. F. A.,
    3. Hoogerhout P.,
    4. Brugghe H. F.,
    5. Timmermans H. A. M.,
    6. de Jong A.,
    7. Meiring H.,
    8. ten Hove J.,
    9. Hennink W. E.,
    10. Crommelin D. J. A.,
    11. Jiskoot W.

    Identification of Formaldehyde-Induced Modifications in Proteins: Reactions with Model Peptides. J. Biol. Chem. 2004, 279 (8), 6235–6243.

    OpenUrlAbstract/FREE Full Text
48. 48.↵
    1. Natsch A.,
    2. Gfeller H.,
    3. Rothaupt M.,
    4. Ellis G.

    Utility and Limitations of a Peptide Reactivity Assay to Predict Fragrance Allergens In Vitro. Toxicol. In Vitro 2007, 21 (7), 1220–1226.

    OpenUrlCrossRefPubMedWeb of Science
49. 49.↵
    International Conference on Harmonisation. ICH Guideline Q9: Quality Risk Management. ICH: Geneva, 2005.