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Toulouse JL, Abraham SMJ, Kadnikova N, Bastien D, Gauchot V, Schmitzer AR, Pelletier JN. Investigation of Classical Organic and Ionic Liquid Cosolvents for Early-Stage Screening in Fragment-Based Inhibitor Design with Unrelated Bacterial and Human Dihydrofolate Reductases. Assay Drug Dev Technol 2017; 15:141-153. [PMID: 28426233 DOI: 10.1089/adt.2016.768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug design by methods such as fragment screening requires effective solubilization of millimolar concentrations of small organic compounds while maintaining the properties of the biological target. We investigate four organic solvents and three 1-butyl-3-methylimidazolium (BMIm)-based ionic liquids (ILs) as cosolvents to establish conditions for screening two structurally unrelated dihydrofolate reductases (DHFRs) that are prime drug targets. Moderate concentrations (10%-15%) of cosolvents had little effect on inhibition of the microbial type II R67 DHFR and of human DHFR (hDHFR), while higher concentrations of organic cosolvents generally decreased activity of both DHFRs. In contrast, a specific IL conserved the activity of one DHFR, while severely reducing the activity of the other, and vice versa, illustrating the differing effect of ILs on distinct protein folds. Most of the cosolvents investigated preserved the fold of R67 DHFR and had little effect on binding of the cofactor NADPH, but reduced the productive affinity for its substrate. In contrast, cosolvents resulted in modest structural destabilization of hDHFR with little effect on productive affinity. We conclude that the organic cosolvents, methanol, dimethylformamide, and dimethylsulfoxide, offer the most balanced conditions for early-stage compound screening as they maintain sufficient biological activity of both DHFRs while allowing for compound dissolution in the millimolar range. However, IL cosolvents showed poor capacity to solubilize organic compounds at millimolar concentrations, mitigating their utility in early-stage screening. Nonetheless, ILs could provide an alternative to classical organic cosolvents when low concentrations of inhibitors are used, as when characterizing higher affinity inhibitors.
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Affiliation(s)
- Jacynthe L Toulouse
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Sarah M J Abraham
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Natalia Kadnikova
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Dominic Bastien
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Vincent Gauchot
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Andreea R Schmitzer
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Joelle N Pelletier
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
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Bastien D, Ebert MCCJC, Forge D, Toulouse J, Kadnikova N, Perron F, Mayence A, Huang TL, Vanden Eynde JJ, Pelletier JN. Fragment-Based Design of Symmetrical Bis-benzimidazoles as Selective Inhibitors of the Trimethoprim-Resistant, Type II R67 Dihydrofolate Reductase. J Med Chem 2012; 55:3182-92. [DOI: 10.1021/jm201645r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic Bastien
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Maximilian C. C. J. C. Ebert
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Delphine Forge
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Jacynthe Toulouse
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Natalia Kadnikova
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Florent Perron
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Annie Mayence
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Tien L. Huang
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | | | - Joelle N. Pelletier
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
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Schmitzer AR, Lépine F, Pelletier JN. Combinatorial exploration of the catalytic site of a drug-resistant dihydrofolate reductase: creating alternative functional configurations. Protein Eng Des Sel 2004; 17:809-19. [PMID: 15576381 DOI: 10.1093/protein/gzh090] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have applied a global approach to enzyme active site exploration, where multiple mutations were introduced combinatorially at the active site of Type II R67 dihydrofolate reductase (R67 DHFR), creating numerous new active site environments within a constant framework. By this approach, we combinatorially modified all 16 principal amino acids that constitute the active site of this enzyme. This approach is fundamentally different from active site point mutation in that the native active site context is no longer accounted for. Among the 1536 combinatorially mutated active site variants of R67 DHFR we created, we selected and kinetically characterized three variants with highly altered active site compositions. We determined that they are of high fitness, as defined by a complex function consisting jointly of catalytic activity and resistance to trimethoprim. The k(cat) and K(M) values were similar to those for the native enzyme. The favourable Delta(DeltaG) values obtained (ranging from -0.72 to -1.08 kcal/mol) suggest that, despite their complex mutational pattern, no fundamental change in the catalytic mechanism has occurred. We illustrate that combinatorial active site mutagenesis can allow for the creation of compensatory mutations that could not be predicted and thus provides a route for more extensive exploration of functional sequence space than is allowed by point mutation.
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Affiliation(s)
- Andreea R Schmitzer
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, H3C 3J7, Montréal, Québec, Canada
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