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Peiró Cadahía J, Bondebjerg J, Hansen CA, Previtali V, Hansen AE, Andresen TL, Clausen MH. Synthesis and Evaluation of Hydrogen Peroxide Sensitive Prodrugs of Methotrexate and Aminopterin for the Treatment of Rheumatoid Arthritis. J Med Chem 2018; 61:3503-3515. [PMID: 29605999 DOI: 10.1021/acs.jmedchem.7b01775] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A series of novel hydrogen peroxide sensitive prodrugs of methotrexate (MTX) and aminopterin (AMT) were synthesized and evaluated for therapeutic efficacy in mice with collagen induced arthritis (CIA) as a model of chronic rheumatoid arthritis (RA). The prodrug strategy selected is based on ROS-labile 4-methylphenylboronic acid promoieties linked to the drugs via a carbamate linkage or a direct C-N bond. Activation under pathophysiological concentrations of H2O2 proved to be effective, and prodrug candidates were selected in agreement with relevant in vitro physicochemical and pharmacokinetic assays. Selected candidates showed moderate to good solubility, high chemical and enzymatic stability, and therapeutic efficacy comparable to the parent drugs in the CIA model. Importantly, the prodrugs displayed the expected safer toxicity profile and increased therapeutic window compared to MTX and AMT while maintaining a comparable therapeutic efficacy, which is highly encouraging for future use in RA patients.
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Affiliation(s)
- Jorge Peiró Cadahía
- Center for Nanomedicine & Theranostics, Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark
| | - Jon Bondebjerg
- MC2 Therapeutics , Agern Alle 24-26 , 2970 Hørsholm , Denmark
| | | | - Viola Previtali
- Center for Nanomedicine & Theranostics, Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark
| | - Anders E Hansen
- Center for Nanomedicine & Theranostics, Department of Micro- and Nanotechnology , Technical University of Denmark , Ørsteds Plads, Building 345 , DK-2800 Kongens Lyngby , Denmark
| | - Thomas L Andresen
- Center for Nanomedicine & Theranostics, Department of Micro- and Nanotechnology , Technical University of Denmark , Ørsteds Plads, Building 345 , DK-2800 Kongens Lyngby , Denmark
| | - Mads H Clausen
- Center for Nanomedicine & Theranostics, Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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Peralta-Yahya P, Carter BT, Lin H, Tao H, Cornish VW. High-throughput selection for cellulase catalysts using chemical complementation. J Am Chem Soc 2009; 130:17446-52. [PMID: 19053460 DOI: 10.1021/ja8055744] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient enzymatic hydrolysis of lignocellulosic material remains one of the major bottlenecks to cost-effective conversion of biomass to ethanol. Improvement of glycosylhydrolases, however, is limited by existing medium-throughput screening technologies. Here, we report the first high-throughput selection for cellulase catalysts. This selection was developed by adapting chemical complementation to provide a growth assay for bond cleavage reactions. First, a URA3 counter selection was adapted to link chemical dimerizer activated gene transcription to cell death. Next, the URA3 counter selection was shown to detect cellulase activity based on cleavage of a tetrasaccharide chemical dimerizer substrate and decrease in expression of the toxic URA3 reporter. Finally, the utility of the cellulase selection was assessed by isolating cellulases with improved activity from a cellulase library created by family DNA shuffling. This application provides further evidence that chemical complementation can be readily adapted to detect different enzymatic activities for important chemical transformations for which no natural selection exists. Because of the large number of enzyme variants that selections can now test as compared to existing medium-throughput screens for cellulases, this assay has the potential to impact the discovery of improved cellulases and other glycosylhydrolases for biomass conversion from libraries of cellulases created by mutagenesis or obtained from natural biodiversity.
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Kitaoka M, Honda Y, Fushinobu S, Hidaka M, Katayama T, Yamamoto K. Conversion of inverting glycoside hydrolases into catalysts for synthesizing glycosides employing a glycosynthase strategy. TRENDS GLYCOSCI GLYC 2009. [DOI: 10.4052/tigg.21.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Corson TW, Aberle N, Crews CM. Design and Applications of Bifunctional Small Molecules: Why Two Heads Are Better Than One. ACS Chem Biol 2008; 3:677-692. [PMID: 19112665 DOI: 10.1021/cb8001792] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Induction of protein--protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein molecules together for enhanced or novel biological effect. The first such bifunctional molecules were the rapamycin- and FK506-based "chemical inducers of dimerization", but the field has since expanded with new molecules and new applications in chemical genetics and cell biology. Examples include coumermycin-mediated gyrase B dimerization, proteolysis targeting chimeric molecules (PROTACs), drug hybrids, and strategies for exploiting multivalency in toxin binding and antibody recruitment. This Review discusses these and other advances in the design and use of bifunctional small molecules and potential strategies for future systems.
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Affiliation(s)
| | | | - Craig M. Crews
- Department of Molecular, Cellular & Developmental Biology
- Departments of Chemistry and Pharmacology, Yale University, New Haven, Connecticut 06511
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A universal screening assay for glycosynthases: directed evolution of glycosynthase XynB2(E335G) suggests a general path to enhance activity. ACTA ACUST UNITED AC 2008; 15:546-51. [PMID: 18559265 DOI: 10.1016/j.chembiol.2008.05.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 04/30/2008] [Accepted: 05/02/2008] [Indexed: 11/20/2022]
Abstract
Glycosynthases are catalytic mutants of mainly retaining glycoside hydrolases that catalyze the synthesis of oligosaccharides from their corresponding glycosyl-fluoride donors and suitable acceptors. Here we describe the development of a general, high-throughput screening procedure for glycosynthase activity, which is based on the release of hydrofluoric acid, a by-product of all glycosynthase reactions. This assay is sensitive, does not require the synthesis of special chromophoric or modified substrates, and, most importantly, is applicable for all glycosynthases. We used this screening procedure on error-prone PCR libraries to isolate improved glycosynthase variants of XynB2(E335G) glycosynthase, a family 52 beta-xylosidase from Geobacillus stearothermophilus. The improved variants exhibited higher K(M) values toward the acceptor and the donor, suggesting that enzyme-product release is rate determining for k(cat).
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Tao H, Peralta-Yahya P, Decatur J, Cornish VW. Characterization of a new glycosynthase cloned by using chemical complementation. Chembiochem 2008; 9:681-4. [PMID: 18330853 DOI: 10.1002/cbic.200700545] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Haiyan Tao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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