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Rouleau FD, Dubé AK, Gagnon-Arsenault I, Dibyachintan S, Pageau A, Després PC, Lagüe P, Landry CR. Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate. PLoS Genet 2024; 20:e1011252. [PMID: 38683847 PMCID: PMC11125491 DOI: 10.1371/journal.pgen.1011252] [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: 10/17/2023] [Revised: 05/24/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Pneumocystis jirovecii is a fungal pathogen that causes pneumocystis pneumonia, a disease that mainly affects immunocompromised individuals. This fungus has historically been hard to study because of our inability to grow it in vitro. One of the main drug targets in P. jirovecii is its dihydrofolate reductase (PjDHFR). Here, by using functional complementation of the baker's yeast ortholog, we show that PjDHFR can be inhibited by the antifolate methotrexate in a dose-dependent manner. Using deep mutational scanning of PjDHFR, we identify mutations conferring resistance to methotrexate. Thirty-one sites spanning the protein have at least one mutation that leads to resistance, for a total of 355 high-confidence resistance mutations. Most resistance-inducing mutations are found inside the active site, and many are structurally equivalent to mutations known to lead to resistance to different antifolates in other organisms. Some sites show specific resistance mutations, where only a single substitution confers resistance, whereas others are more permissive, as several substitutions at these sites confer resistance. Surprisingly, one of the permissive sites (F199) is without direct contact to either ligand or cofactor, suggesting that it acts through an allosteric mechanism. Modeling changes in binding energy between F199 mutants and drug shows that most mutations destabilize interactions between the protein and the drug. This evidence points towards a more important role of this position in resistance than previously estimated and highlights potential unknown allosteric mechanisms of resistance to antifolate in DHFRs. Our results offer unprecedented resources for the interpretation of mutation effects in the main drug target of an uncultivable fungal pathogen.
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Affiliation(s)
- Francois D. Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Alexandre K. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
| | - Soham Dibyachintan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Alicia Pageau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Philippe C. Després
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Patrick Lagüe
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
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Sah S, Varshney U. Methionyl-tRNA formyltransferase utilizes 10-formyldihydrofolate as an alternative substrate and impacts antifolate drug action. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36745551 DOI: 10.1099/mic.0.001297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methionyl-tRNA formyltransferase (Fmt)-mediated formylation of Met-tRNAfMet to fMet-tRNAfMet is crucial for efficient initiation of translation in bacteria and the eukaryotic organelles. Folate dehydrogenase-cyclohydrolase (FolD), a bifunctional enzyme, carries out conversion of 5,10-methylene tetrahydrofolate (5,10-CH2-THF) to 10-formyl-THF (10-CHO-THF), a metabolite utilized by Fmt as a formyl group donor. In this study, using in vivo and in vitro approaches, we show that 10-CHO-DHF may also be utilized by Fmt as an alternative substrate (formyl group donor) to formylate Met-tRNAfMet. Dihydrofolate (DHF) formed as a by-product in the in vitro assay was verified by LC-MS/MS analysis. FolD-deficient mutants and Fmt over-expressing strains were more sensitive to trimethoprim (TMP) than the ∆fmt strain, suggesting that the domino effect of TMP leads to inhibition of protein synthesis and strain growth. Antifolate treatment to Escherichia coli showed a decrease in the reduced folate species (THF, 5,10-CH2-THF, 5-CH3-THF, 5,10-CH+-THF and 5-CHO-THF) and increase in the oxidized folate species (folic acid and DHF). In cells, 10-CHO-DHF and 10-CHO-folic acid were enriched in the stationary phase. This suggests that 10-CHO-DHF is a bioactive metabolite in the folate pathway for generating other folate intermediates and fMet-tRNAfMet.
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Affiliation(s)
- Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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Comparison of Different Clinical Chemotherapeutical Agents’ Toxicity and Cell Response on Mesenchymal Stem Cells and Cancer Cells. Cells 2022; 11:cells11192942. [PMID: 36230904 PMCID: PMC9563435 DOI: 10.3390/cells11192942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/08/2022] [Accepted: 09/17/2022] [Indexed: 11/29/2022] Open
Abstract
Mesenchymal stem cells (MSCs) or fibroblasts are one of the most abundant cell types in the tumor microenvironment (TME) exerting various anti- and pro-apoptotic effects during tumorigenesis, invasion, and drug treatment. Despite the recently discovered importance of MSCs in tumor progression and therapy, the response of these cells to chemotherapeutics compared to cancer cells is rarely investigated. A widely accepted view is that these naive MSCs have higher drug tolerance than cancer cells due to a significantly lower proliferation rate. Here, we examine the differences and similarities in the sensitivity of MSCs and cancer cells to nine diverse chemotherapy agents and show that, although MSCs have a slower cell cycle, these cells are still sensitive to various drugs. Surprisingly, MSCs showed similar sensitivity to a panel of compounds, however, suffered fewer DNA double-stranded breaks, did not enter into a senescent state, and was virtually incapable of apoptosis. Our results suggest that MSCs and cancer cells have different cell fates after drug treatment, and this could influence therapy outcome. These findings could help design drug combinations targeting both MSCs and cancer cells in the TME.
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Tilsed CM, Fisher SA, Nowak AK, Lake RA, Lesterhuis WJ. Cancer chemotherapy: insights into cellular and tumor microenvironmental mechanisms of action. Front Oncol 2022; 12:960317. [PMID: 35965519 PMCID: PMC9372369 DOI: 10.3389/fonc.2022.960317] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/01/2022] [Indexed: 12/12/2022] Open
Abstract
Chemotherapy has historically been the mainstay of cancer treatment, but our understanding of what drives a successful therapeutic response remains limited. The diverse response of cancer patients to chemotherapy has been attributed principally to differences in the proliferation rate of the tumor cells, but there is actually very little experimental data supporting this hypothesis. Instead, other mechanisms at the cellular level and the composition of the tumor microenvironment appear to drive chemotherapy sensitivity. In particular, the immune system is a critical determinant of chemotherapy response with the depletion or knock-out of key immune cell populations or immunological mediators completely abrogating the benefits of chemotherapy in pre-clinical models. In this perspective, we review the literature regarding the known mechanisms of action of cytotoxic chemotherapy agents and the determinants of response to chemotherapy from the level of individual cells to the composition of the tumor microenvironment. We then summarize current work toward the development of dynamic biomarkers for response and propose a model for a chemotherapy sensitive tumor microenvironment.
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Affiliation(s)
- Caitlin M. Tilsed
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
| | - Scott A. Fisher
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
| | - Anna K. Nowak
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, Nedlands, WA, Australia
- Medical School, University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Richard A. Lake
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
| | - W. Joost Lesterhuis
- National Centre for Asbestos Related Diseases, Institute for Respiratory Health, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
- Telethon Kids Institute, University of Western Australia, West Perth, WA, Australia
- *Correspondence: W. Joost Lesterhuis,
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Abstract
Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.
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Oiwa K, Hosono N, Nishi R, Scotto L, O'Connor OA, Yamauchi T. Characterization of newly established Pralatrexate-resistant cell lines and the mechanisms of resistance. BMC Cancer 2021; 21:879. [PMID: 34332580 PMCID: PMC8325835 DOI: 10.1186/s12885-021-08607-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/16/2021] [Indexed: 11/20/2022] Open
Abstract
Background Pralatrexate (PDX) is a novel antifolate approved for the treatment of patients with relapsed/refractory peripheral T-cell lymphoma, but some patients exhibit intrinsic resistance or develop acquired resistance. Here, we evaluated the mechanisms underlying acquired resistance to PDX and explored potential therapeutic strategies to overcome PDX resistance. Methods To investigate PDX resistance, we established two PDX-resistant T-lymphoblastic leukemia cell lines (CEM and MOLT4) through continuous exposure to increasing doses of PDX. The resistance mechanisms were evaluated by measuring PDX uptake, apoptosis induction and folate metabolism-related protein expression. We also applied gene expression analysis and methylation profiling to identify the mechanisms of resistance. We then explored rational drug combinations using a spheroid (3D)-culture assay. Results Compared with their parental cells, PDX-resistant cells exhibited a 30-fold increase in half-maximal inhibitory concentration values. Induction of apoptosis by PDX was significantly decreased in both PDX-resistant cell lines. Intracellular uptake of [14C]-PDX decreased in PDX-resistant CEM cells but not in PDX-resistant MOLT4 cells. There was no significant change in expression of dihydrofolate reductase (DHFR) or folylpolyglutamate synthetase (FPGS). Gene expression array analysis revealed that DNA-methyltransferase 3β (DNMT3B) expression was significantly elevated in both cell lines. Gene set enrichment analysis revealed that adipogenesis and mTORC1 signaling pathways were commonly upregulated in both resistant cell lines. Moreover, CpG island hypermethylation was observed in both PDX resistant cells lines. In the 3D-culture assay, decitabine (DAC) plus PDX showed synergistic effects in PDX-resistant cell lines compared with parental lines. Conclusions The resistance mechanisms of PDX were associated with reduced cellular uptake of PDX and/or overexpression of DNMT3B. Epigenetic alterations were also considered to play a role in the resistance mechanism. The combination of DAC and PDX exhibited synergistic activity, and thus, this approach might improve the clinical efficacy of PDX. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08607-9.
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Affiliation(s)
- Kana Oiwa
- Department of Hematology and Oncology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
| | - Naoko Hosono
- Department of Hematology and Oncology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan.
| | - Rie Nishi
- Department of Hematology and Oncology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
| | - Luigi Scotto
- The Center of Lymphoid Malignancy, Columbia University Medical Center, College of Physicians and Surgeons, 630 West 168th St, New York, NY, 10032, USA
| | - Owen A O'Connor
- The Center of Lymphoid Malignancy, Columbia University Medical Center, College of Physicians and Surgeons, 630 West 168th St, New York, NY, 10032, USA.,Department of Medicine, Division of Hematology and Oncology, University of Virginia, 1215 Lee Street, Charlottesville, VA, 22903, USA
| | - Takahiro Yamauchi
- Department of Hematology and Oncology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
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Park J, Obeng J, Spezia P, Huang J, Morrone DJ. Student design and characterization of visible DHFR fusions for biochemistry tools to improve learning during lab exercises. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:560-569. [PMID: 33830617 DOI: 10.1002/bmb.21508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Student feedback from an undergraduate biochemistry lab course suggested the use of visibly traceable proteins may assist learning. Based on this feedback, we used guided inquiry lab exercises where students developed and characterized a suite of fluorescent protein-dihydrofolate reductase (DHFR) fusions as tools for a biochemistry teaching lab. In contrast to the unfused versions, members of this suite are well-expressed, soluble, visible, highly stable, and easily characterized. The color of mCherry and EGFP fluorescent fusions with microbial DHFR allows students to visibly track their target protein from expression through purification under ambient light, while fusions with BFP are visible under UV-light. Fusions were made to both wild-type and kinetically enhanced DHFR variants. Importantly, we found that fluorescent protein fusions with DHFR did not kinetically interfere as the KM and kcat values were not remarkably altered from the unfused variant. With these fusions, students can easily measure kinetic parameters under steady-state conditions with readily available substrate and common laboratory spectrophotometers. Additionally, students also determined IC50 values of trimethoprim for DHFR. These exercises can be completed in a series of up to six lab periods and we have included the protocols for instructors who wish undertake a similar series of experiments in their biochemistry teaching labs. Using these visible fusion enzymes with subsequent students, we observed potential learning gains on a course assessment and received positive student feedback. We suggest that the often over-looked element of visual cues in a biochemistry lab may be an exploitable component of learning.
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Affiliation(s)
- Junyun Park
- Department of Basic Sciences, University of Health Sciences and Pharmacy in St. Louis, St. Louis, Missouri, USA
| | - Jeremiah Obeng
- Department of Basic Sciences, University of Health Sciences and Pharmacy in St. Louis, St. Louis, Missouri, USA
| | - Peter Spezia
- Department of Basic Sciences, University of Health Sciences and Pharmacy in St. Louis, St. Louis, Missouri, USA
| | - Jonathan Huang
- Department of Basic Sciences, University of Health Sciences and Pharmacy in St. Louis, St. Louis, Missouri, USA
| | - Dana J Morrone
- Department of Basic Sciences, University of Health Sciences and Pharmacy in St. Louis, St. Louis, Missouri, USA
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Park S, Pascua E, Lindquist KC, Kimberlin C, Deng X, Mak YSL, Melton Z, Johnson TO, Lin R, Boldajipour B, Abraham RT, Pons J, Sasu BJ, Van Blarcom TJ, Chaparro-Riggers J. Direct control of CAR T cells through small molecule-regulated antibodies. Nat Commun 2021; 12:710. [PMID: 33514714 PMCID: PMC7846603 DOI: 10.1038/s41467-020-20671-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/02/2020] [Indexed: 01/30/2023] Open
Abstract
Antibody-based therapeutics have experienced a rapid growth in recent years and are now utilized in various modalities spanning from conventional antibodies, antibody-drug conjugates, bispecific antibodies to chimeric antigen receptor (CAR) T cells. Many next generation antibody therapeutics achieve enhanced potency but often increase the risk of adverse events. Antibody scaffolds capable of exhibiting inducible affinities could reduce the risk of adverse events by enabling a transient suspension of antibody activity. To demonstrate this, we develop conditionally activated, single-module CARs, in which tumor antigen recognition is directly modulated by an FDA-approved small molecule drug. The resulting CAR T cells demonstrate specific cytotoxicity of tumor cells comparable to that of traditional CARs, but the cytotoxicity is reversibly attenuated by the addition of the small molecule. The exogenous control of conditional CAR T cell activity allows continual modulation of therapeutic activity to improve the safety profile of CAR T cells across all disease indications.
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Affiliation(s)
- Spencer Park
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Lyell Immunopharma, South San Francisco, CA USA
| | - Edward Pascua
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA
| | | | - Christopher Kimberlin
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Asher Bio, South San Francisco, CA USA
| | - Xiaodi Deng
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Dren Bio, San Carlos, CA USA
| | - Yvonne S. L. Mak
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Zea Melton
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | | | - Regina Lin
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Bijan Boldajipour
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Lyell Immunopharma, South San Francisco, CA USA
| | - Robert T. Abraham
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Vividion Therapeutics, San Diego, CA USA
| | - Jaume Pons
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: ALX Oncology, Burlingame, CA USA
| | - Barbra Johnson Sasu
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Thomas J. Van Blarcom
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
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Eck T, Patel S, Candela T, Leon H K, Little M, Reis NE, Liyanagunawardana U, Gubler U, Janson CA, Catalano J, Goodey NM. Mutational analysis confirms the presence of distal inhibitor-selectivity determining residues in B. stearothermophilus dihydrofolate reductase. Arch Biochem Biophys 2020; 692:108545. [PMID: 32810476 PMCID: PMC10727455 DOI: 10.1016/j.abb.2020.108545] [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: 05/22/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022]
Abstract
Many antibacterial and antiparasitic drugs work by competitively inhibiting dihydrofolate reductase (DHFR), a vital enzyme in folate metabolism. The interactions between inhibitors and DHFR active site residues are known in many homologs but the contributions from distal residues are less understood. Identifying distal residues that aid in inhibitor binding can improve targeted drug development programs by accounting for distant influences that may be less conserved and subject to frequent resistance causing mutations. Previously, a novel, homology-based, computational approach that mines ligand inhibition data was used to predict residues involved in inhibitor selectivity in the DHFR family. Expectedly, some inhibitor selectivity determining residue positions were predicted to lie in the active site and coincide with experimentally known inhibitor selectivity determining positions. However, other residues that group spatially in clusters distal to the active site have not been previously investigated. In this study, the effect of introducing amino acid substitutions at one of these predicted clusters (His38-Ala39-Ile40) on the inhibitor selectivity profile in Bacillus stearothermophilus dihydrofolate reductase (Bs DHFR) was investigated. Mutations were introduced into these cluster positions to change sidechain chemistry and size. We determined kcat and KM values and measured KD values at equilibrium for two competitive DHFR inhibitors, trimethoprim (TMP) and pyrimethamine (PYR). Mutations in the His38-Ala39-Ile40 cluster significantly impacted inhibitor binding and TMP/PYR selectivity - seven out of nine mutations resulted in tighter binding to PYR when compared to TMP. These data suggest that the His38-Ala39-Ile40 cluster is a distal inhibitor selectivity determining region that favors PYR binding in Bs DHFR and, possibly, throughout the DHFR family.
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Affiliation(s)
- Tyler Eck
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Seema Patel
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Thomas Candela
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Katherine Leon H
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Michael Little
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Natalia E Reis
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | | | - Ueli Gubler
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Cheryl A Janson
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Jaclyn Catalano
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Nina M Goodey
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA.
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Rana RM, Rampogu S, Abid NB, Zeb A, Parate S, Lee G, Yoon S, Kim Y, Kim D, Lee KW. In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics. Molecules 2020; 25:molecules25153510. [PMID: 32752079 PMCID: PMC7435474 DOI: 10.3390/molecules25153510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 11/16/2022] Open
Abstract
Drug resistance is a core issue in cancer chemotherapy. A known folate antagonist, methotrexate (MTX) inhibits human dihydrofolate reductase (hDHFR), the enzyme responsible for the catalysis of 7,8-dihydrofolate reduction to 5,6,7,8-tetrahydrofolate, in biosynthesis and cell proliferation. Structural change in the DHFR enzyme is a significant cause of resistance and the subsequent loss of MTX. In the current study, wild type hDHFR and double mutant (engineered variant) F31R/Q35E (PDB ID: 3EIG) were subject to computational study. Structure-based pharmacophore modeling was carried out for wild type (WT) and mutant (MT) (variant F31R/Q35E) hDHFR structures by generating ten models for each. Two pharmacophore models, WT-pharma and MT-pharma, were selected for further computations, and showed excellent ROC curve quality. Additionally, the selected pharmacophore models were validated by the Guner-Henry decoy test method, which yielded high goodness of fit for WT-hDHFR and MT-hDHFR. Using a SMILES string of MTX in ZINC15 with the selections of 'clean', in vitro and in vivo options, 32 MTX-analogs were obtained. Eight analogs were filtered out due to their drug-like properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment tests and Lipinski's Rule of five. WT-pharma and MT-pharma were further employed as a 3D query in virtual screening with drug-like MTX analogs. Subsequently, seven screening hits along with a reference compound (MTX) were subjected to molecular docking in the active site of WT- and MT-hDHFR. Through a clustering analysis and examination of protein-ligand interactions, one compound was found with a ChemPLP fitness score greater than that of MTX (reference compound). Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM/PBSA binding free energy. In conclusion, we report on an MTX analog which is capable of inhibiting hDHFR in wild type form, as well as in cases where the enzyme acquires resistance to drugs during chemotherapy treatment.
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Affiliation(s)
- Rabia Mukhtar Rana
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Noman Bin Abid
- Division of Life Science and Applied Life Science (BK 21), College of Natural Sciences, Gyeongsang National University, Jinju 52828, Korea;
| | - Amir Zeb
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Shraddha Parate
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Gihwan Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Sanghwa Yoon
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Yumi Kim
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Donghwan Kim
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
- Correspondence: ; Tel.: +82-55-772-1360
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11
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Duff MR, Gabel SA, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. The Structural Basis for Nonsteroidal Anti-Inflammatory Drug Inhibition of Human Dihydrofolate Reductase. J Med Chem 2020; 63:8314-8324. [PMID: 32658475 DOI: 10.1021/acs.jmedchem.0c00546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although nonsteroidal anti-inflammatory drugs (NSAIDs) target primarily cyclooxygenase enzymes, a subset of NSAIDs containing carboxylate groups also has been reported to competitively inhibit dihydrofolate reductase (DHFR). In this study, we have characterized NSAID interactions with human DHFR based on kinetic, NMR, and X-ray crystallographic methods. The NSAIDs target a region of the folate binding site that interacts with the p-aminobenzoyl-l-glutamate (pABG) moiety of folate and inhibit cooperatively with ligands that target the adjacent pteridine-recognition subsite. NSAIDs containing benzoate or salicylate groups were identified as having the highest potency. Among those tested, diflunisal, a salicylate derivative not previously identified to have anti-folate activity, was found to have a Ki of 34 μM, well below peak plasma diflunisal levels reached at typical dosage levels. The potential of these drugs to interfere with the inflammatory process by multiple pathways introduces the possibility of further optimization to design dual-targeted analogs.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Scott A Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, Durham, North Carolina 27709, United States
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12
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Sah S, Shah RA, Govindan A, Varada R, Rex K, Varshney U. Utilisation of 10-formyldihydrofolate as substrate by dihydrofolate reductase (DHFR) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) tranformylase/IMP cyclohydrolase (PurH) in Escherichia coli. MICROBIOLOGY-SGM 2019; 164:982-991. [PMID: 29799386 DOI: 10.1099/mic.0.000671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dihydrofolate reductase (DHFR) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase (PurH) play key roles in maintaining folate pools in cells, and are targets of antimicrobial and anticancer drugs. While the activities of bacterial DHFR and PurH on their classical substrates (DHF and 10-CHO-THF, respectively) are known, their activities and kinetic properties of utilisation of 10-CHO-DHF are unknown. We have determined the kinetic properties (k cat/K m) of conversion of 10-CHO-DHF to 10-CHO-THF by DHFR, and to DHF by PurH. We show that DHFR utilises 10-CHO-DHF about one third as efficiently as it utilises DHF. The 10-CHO-DHF is also utilised (as a formyl group donor) by PurH albeit slightly less efficiently than 10-CHO-THF. The utilisation of 10-CHO-DHF by DHFR is ~50 fold more efficient than its utilisation by PurH. A folate deficient Escherichia coli (∆pabA) grows well when supplemented with adenine, glycine, thymine and methionine, the metabolites that arise from the one-carbon metabolic pathway. Notably, when the ∆pabA strain harboured a folate transporter, it grew in the presence of 10-CHO-DHF alone, suggesting that it (10-CHO-DHF) can enter one-carbon metabolic pathway to provide the required metabolites. Thus, our studies reveal that both DHFR and PurH could utilise 10-CHO-DHF for folate homeostasis in E. coli.
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Affiliation(s)
- Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Ashwin Govindan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Kervin Rex
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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13
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Dihydrofolate reductase inhibition effect of 5-substituted pyrido[2,3-d]pyrimidines: Synthesis, antitumor activity and molecular modeling study. Bioorg Chem 2019; 90:103076. [DOI: 10.1016/j.bioorg.2019.103076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
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14
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Toulouse J, Yachnin BJ, Ruediger EH, Deon D, Gagnon M, Saint-Jacques K, Ebert MCCC, Forge D, Bastien D, Colin DY, Vanden Eynde JJ, Marinier A, Berghuis AM, Pelletier JN. Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues. ACS OMEGA 2019; 4:10056-10069. [PMID: 31460098 PMCID: PMC6648814 DOI: 10.1021/acsomega.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/18/2023]
Abstract
The worldwide use of the broad-spectrum antimicrobial trimethoprim (TMP) has induced the rise of TMP-resistant microorganisms. In addition to resistance-causing mutations of the microbial chromosomal dihydrofolate reductase (Dfr), the evolutionarily and structurally unrelated type II Dfrs (DfrBs) have been identified in TMP-resistant microorganisms. DfrBs are intrinsically TMP-resistant and allow bacterial proliferation when the microbial chromosomal Dfr is TMP-inhibited, making these enzymes important targets for inhibitor development. Furthermore, DfrBs occur in multiresistance plasmids, potentially accelerating their dissemination. We previously reported symmetrical bisbenzimidazoles that are the first selective inhibitors of the only well-characterized DfrB, DfrB1. Here, their diversification provides a new series of inhibitors (K i = 1.7-12.0 μM). Our results reveal two prominent features: terminal carboxylates and inhibitor length allow the establishment of essential interactions with DfrB1. Two crystal structures demonstrate the simultaneous binding of two inhibitor molecules in the symmetrical active site. Observations of those dimeric inhibitors inspired the design of monomeric analogues, binding in a single copy yet offering similar inhibition potency (K i = 1.1 and 7.4 μM). Inhibition of a second member of the DfrB family, DfrB4, suggests the generality of these inhibitors. These results provide key insights into inhibition of the highly TMP-resistant DfrBs, opening avenues to downstream development of antibiotics for combatting this emergent source of resistance.
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Affiliation(s)
- Jacynthe
L. Toulouse
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Brahm J. Yachnin
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Edward H. Ruediger
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Daniel Deon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Marc Gagnon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Kévin Saint-Jacques
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- Département
de Chimie, Université de Sherbrooke, Sherbrooke J1K 0A5, Quebec, Canada
| | | | - Delphine Forge
- Laboratoire
de Chimie Organique, Université de
Mons, Mons 7000, Belgium
| | - Dominic Bastien
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Damien Y. Colin
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | | | - Anne Marinier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Albert M. Berghuis
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
- E-mail: . Phone: 514-343-2124. Fax: 514-343-7586
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15
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Yachnin BJ, Khare SD. Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme. Protein Eng Des Sel 2017; 30:321-331. [PMID: 28160000 PMCID: PMC6283397 DOI: 10.1093/protein/gzx005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Carboxypeptidase G2 (CPG2) is an Food and Drug Administration (FDA)-approved enzyme drug used to treat methotrexate (MTX) toxicity in cancer patients receiving MTX treatment. It has also been used in directed enzyme-prodrug chemotherapy, but this strategy has been hampered by off-site activation of the prodrug by the circulating enzyme. The development of a tumor protease activatable CPG2, which could be achieved using a circular permutation of CPG2 fused to an inactivating 'prodomain', would aid in these applications. We report the development of a protease accessibility-based screen to identify candidate sites for circular permutation in proximity of the CPG2 active site. The resulting six circular permutants showed similar expression, structure, thermal stability, and, in four cases, activity levels compared to the wild-type enzyme. We rationalize these results based on structural models of the permutants obtained using the Rosetta software. We developed a cell growth-based selection system, and demonstrated that when fused to periplasm-directing signal peptides, one of our circular permutants confers MTX resistance in Escherichia coli with equal efficiency as the wild-type enzyme. As the permutants have similar properties to wild-type CPG2, these enzymes are promising starting points for the development of autoinhibited, protease-activatable zymogen forms of CPG2 for use in therapeutic contexts.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | - Sagar D. Khare
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
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16
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Quaglia D, Ebert MCCJC, Mugford PF, Pelletier JN. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening. PLoS One 2017; 12:e0171741. [PMID: 28178357 PMCID: PMC5298319 DOI: 10.1371/journal.pone.0171741] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/25/2017] [Indexed: 12/29/2022] Open
Abstract
The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A), the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random). Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells.
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Affiliation(s)
- Daniela Quaglia
- Département de Chimie, Université de Montréal, Montréal, QC, Canada
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
| | - Paul F. Mugford
- DSM Nutritional Products, 101 Research Drive, Dartmouth, NS, Canada
| | - Joelle N. Pelletier
- Département de Chimie, Université de Montréal, Montréal, QC, Canada
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
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17
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Bukar N, Zhao SS, Charbonneau DM, Pelletier JN, Masson JF. Influence of the Debye length on the interaction of a small molecule-modified Au nanoparticle with a surface-bound bioreceptor. Chem Commun (Camb) 2014; 50:4947-50. [DOI: 10.1039/c4cc01423e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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18
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Ratel M, Provencher-Girard A, Zhao SS, Breault-Turcot J, Labrecque-Carbonneau J, Branca M, Pelletier JN, Schmitzer AR, Masson JF. Imidazolium-based ionic liquid surfaces for biosensing. Anal Chem 2013; 85:5770-7. [PMID: 23706008 DOI: 10.1021/ac400386z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionic liquid self-assembled monolayers (SAM) were designed and applied for binding streptavidin, promoting affinity biosensing and enzyme activity on gold surfaces of sensors. The synthesis of 1-((+)-biotin)pentanamido)propyl)-3-(12-mercaptododecyl)-imidazolium bromide, a biotinylated ionic liquid (IL-biotin), which self-assembles on gold film, afforded streptavidin sensing with surface plasmon resonance (SPR). The IL-biotin-SAM efficiently formed a full streptavidin monolayer. The synthesis of 1-(carboxymethyl)-3-(mercaptododecyl)-imidazoliumbromide, a carboxylated IL (IL-COOH), was used to immobilize anti-IgG to create an affinity biosensor. The IL-COOH demonstrated efficient detection of IgG in the nanomolar concentration range, similar to the alkylthiols SAM and PEG. In addition, the IL-COOH demonstrated low fouling in crude serum, to a level equivalent to PEG. The IL-COOH was further modified with N,N'-bis (carboxymethyl)-l-lysine hydrate to bind copper ions and then, chelate histidine-tagged biomolecules. Human dihydrofolate reductase (hDHFR) was chelated to the modified IL-COOH. By monitoring enzyme activity in situ on the SPR sensor, it was revealed that the IL-COOH SAM improved the activity of hDHFR by 24% in comparison to classical SAM. Thereby, IL-SAM has been synthesized and successfully applied to three important biosensing schemes, demonstrating the advantages of this new class of monolayers.
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Affiliation(s)
- Mathieu Ratel
- Département de Chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, Quebec, Canada H3C 3J7
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19
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Safi M, Lilien RH. Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA. J Chem Inf Model 2012; 52:1529-41. [DOI: 10.1021/ci200626m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Maria Safi
- Department of Computer Science, University of Toronto,
Toronto, Ontario M5S 3G4, Canada
| | - Ryan H. Lilien
- Department of Computer Science, University of Toronto,
Toronto, Ontario M5S 3G4, Canada
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20
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Gómez-Gómez Y, Organista-Nava J, Saavedra-Herrera MV, Rivera-Ramírez AB, Terán-Porcayo MA, Del Carmen Alarcón-Romero L, Illades-Aguiar B, Leyva-Vázquez MA. Survival and risk of relapse of acute lymphoblastic leukemia in a Mexican population is affected by dihydrofolate reductase gene polymorphisms. Exp Ther Med 2012; 3:665-672. [PMID: 22969948 DOI: 10.3892/etm.2012.447] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 12/06/2011] [Indexed: 11/06/2022] Open
Abstract
Dihydrofolate reductase (DHFR) is the major target of methotrexate, a key component in childhood acute lymphoblastic leukemia (ALL) treatment. Polymorphisms in the gene coding for DHFR have been associated with adverse event treatment. This study evaluated the effect of the -A317G and C829T polymorphisms in the DHFR gene on survival and risk of relapse of ALL. Seventy patients with ALL and 100 healthy individuals were genotyped by the polymerase chain reaction-restriction fragment length polymorphism method. An association between the polymorphisms and the risk of relapse was found (p<0.05); patients with the -317G/G genotype were found to have an 8.55 (95% CI 1.84-39.70) higher chance of relapse and carriers of the 829T/T genotype had a 14.0 (95% CI 1.13-172.63) higher chance of relapse. Other variables, such as age and leukocyte count, were associated (p<0.05) with the risk of relapse of the disease. Individuals with the G/G and T/T genotype of the -A317G and C829T polymorphisms had poorer survival compared to other genotype groups (log-rank test; p<0.05). Although preliminary, these data seem to suggest a role for the DHFR polymorphisms in the risk of relapse of ALL and the mortality risk in these patients.
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21
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Zhao SS, Bichelberger MA, Colin DY, Robitaille R, Pelletier JN, Masson JF. Monitoring methotrexate in clinical samples from cancer patients during chemotherapy with a LSPR-based competitive sensor. Analyst 2012; 137:4742-50. [DOI: 10.1039/c2an35839e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Volpato JP, Mayotte N, Fossati E, Guerrero V, Sauvageau G, Pelletier JN. Selectively weakened binding of methotrexate by human dihydrofolate reductase allows rapid ex vivo selection of mammalian cells. J Mol Recognit 2011; 24:188-98. [PMID: 21360609 DOI: 10.1002/jmr.1037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Ex vivo selection of transduced hematopoietic stem cells (HSC) with drug-resistance genes offers the possibility to enrich transduced cells prior to engraftment, toward increased reconstitution in transplant recipients. We evaluated the potential of highly methotrexate (MTX)-resistant variants of human dihydrofolate reductase (hDHFR) for this application. Two subsets of hDHFR variants with reduced affinity for MTX that had been previously identified in a bacterial system were considered: those with substitutions at positions 31, 34, and/or 35, and those with substitutions at position 115. The variants were characterized for their resistance to pemetrexed (PMTX), an antifolate that is related to MTX. We observed a strong correlation between decreased binding to both antifolates, although the identity of specific sequence variations modulated the correlation. We chose a subset of hDHFR variants for tests of ex vivo MTX resistance, taking into consideration their residual specific activity and their decrease in affinity for the related antifolates. Murine myeloid progenitors and other differentiated hematopoietic cells were transduced and exposed to MTX in a nucleotide-free medium. Bone marrow (BM) cells including 15% cells infected with F31R/Q35E were enriched to 98% transduced cells within 6 days of ex vivo selection. hDHFR variant F31R/Q35E allowed a strong ex vivo enrichment upon a short exposure to MTX relative to a less resistant variant of hDHFR, L22Y. We have thus demonstrated that bacterial selection of highly antifolate-resistant hDHFR variants can provide selectable markers for rapid ex vivo enrichment of hematopoietic cells.
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Affiliation(s)
- Jordan P Volpato
- Département de biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
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23
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Sáez-Ayala M, Sánchez-del-Campo L, Montenegro MF, Chazarra S, Tárraga A, Cabezas-Herrera J, Rodríguez-López JN. Comparison of a pair of synthetic tea-catechin-derived epimers: synthesis, antifolate activity, and tyrosinase-mediated activation in melanoma. ChemMedChem 2011; 6:440-9. [PMID: 21302360 DOI: 10.1002/cmdc.201000482] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/23/2010] [Indexed: 11/10/2022]
Abstract
Despite bioavailability issues, tea catechins have emerged as promising chemopreventive agents because of their efficacy in various animal models. We synthesized two catechin-derived compounds, 3-O-(3,4,5-trimethoxybenzoyl)-(-)-catechin (TMCG) and 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG), in an attempt to improve the stability and cellular absorption of tea polyphenols. The antiproliferative and pro-apoptotic activities of both compounds were analyzed with various cancer cell systems, and TMCG, which was easily synthesized in excellent yield, was more active than TMECG in both melanoma and non-melanoma cell lines. TMCG was also a better inhibitor of dihydrofolate reductase and was more efficiently oxidized by tyrosinase, potentially explaining the difference in activity between these epimers.
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Affiliation(s)
- Magalí Sáez-Ayala
- Department of Biochemistry and Molecular Biology A, School of Biology, University of Murcia, and REsearch Unit of Clinical Analysis Service, University Hospital Virgen de la Arrixaca, Avda. Teniente Flomesta, no. 5, 30003 Murcia, Spain
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24
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Bolduc OR, Lambert-Lanteigne P, Colin DY, Zhao SS, Proulx C, Boeglin D, Lubell WD, Pelletier JN, Féthière J, Ong H, Masson JF. Modified peptide monolayer binding His-tagged biomolecules for small ligand screening with SPR biosensors. Analyst 2011; 136:3142-8. [DOI: 10.1039/c1an15235a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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25
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Adding a combination of hydroxycitrate and lipoic acid (METABLOC™) to chemotherapy improves effectiveness against tumor development: experimental results and case report. Invest New Drugs 2010; 30:200-11. [PMID: 20931262 DOI: 10.1007/s10637-010-9552-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 09/23/2010] [Indexed: 12/19/2022]
Abstract
Altered metabolism of cancer first highlighted by Otto Warburg has a long history. Although ignored for a considerable amount of time, it is now receiving substantial attention. We recently published results obtained with a combination of two drugs, lipoic acid and hydroxycitrate, targeting metabolic enzymes particularly affected in cancer: ATP citrate lyase and pyruvate dehydrogenase kinase. This treatment was as efficient as chemotherapy in the three mouse cancer models that were tested. In this work, we asked if our drug combination could be used in conjunction with standard cytotoxic chemotherapy, in particular cisplatin, to improve basic protocol efficacy. A combination of lipoic acid and hydroxycitrate was administered to mice implanted with syngeneic cancer cells, LL/2 lung carcinoma and MBT-2 bladder carcinoma, concommitantly with classical chemotherapy (cisplatin or methotrexate). We demonstrate that the triple combination lipoic acid + hydroxycitrate + cisplatin or methotrexate is more efficient than cisplatin or methotrexate used individually or the combination of lipoic acid and hydroxycitrate administered alone. Of particular note are the results obtained in the treatment of an 80 year-old female who presented with ductal adenocarcinoma of the pancreas accompanied by liver metastases. A treatment course using gemcitabine plus α-lipoic acid and hydroxycitrate gave highly promising results. The in vivo data, coupled with the case study results, suggest a possible advantage in using a treatment targeted at cancer metabolism in association with classical chemotherapy.
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Chung CH, Pohlmann PR, Rothenberg ML, Burkey BB, Parker J, Palka K, Aulino J, Puzanov I, Murphy B. Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma. Head Neck 2010; 33:1804-8. [PMID: 20652976 DOI: 10.1002/hed.21478] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2010] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Recurrent head and neck squamous cell carcinoma (HNSCC) remains a difficult cancer to treat. Here, we describe a patient with HNSCC who had complete response to methotrexate (MTX) after progressing on multiple cytotoxic agents, cetuximab, and AMG-479 (monoclonal antibody against insulin-like growth factor-1 receptor [IGF-1R]). METHODS The clinical information was collected by a retrospective medical record review under an Institutional Review Board-approved protocol. From 4 tumors and 2 normal mucosal epithelia, global gene expression, and IGF-1R and dihydrofolate reductase (DHFR) protein levels were determined. RESULTS Effective target inhibition in the tumor was confirmed by the decreased protein levels of total and phospho-IGF-1R after treatment with AMG-479. Decreased level of DHFR and conversion of a gene expression profile associated with cetuximab-resistance to cetuximab-sensitivity were also observed. CONCLUSION This suggests that the combination of AMG-479 and MTX or cetuximab may be a promising therapeutic approach in refractory HNSCC.
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Affiliation(s)
- Christine H Chung
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Cody V, Pace J, Makin J, Piraino J, Queener SF, Rosowsky A. Correlations of inhibitor kinetics for Pneumocystis jirovecii and human dihydrofolate reductase with structural data for human active site mutant enzyme complexes. Biochemistry 2010; 48:1702-11. [PMID: 19196009 DOI: 10.1021/bi801960h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the role of specific active site residues in conferring selective dihydrofolate reductase (DHFR) inhibition from pathogenic organisms such as Pneumocystis carinii (pc) or Pneumocystis jirovecii (pj), the causative agent in AIDS pneumonia, it is necessary to evaluate the role of these residues in the human enzyme. We report the first kinetic parameters for DHFR from pjDHFR and pcDHFR with methotrexate (MTX), trimethoprim (TMP), and its potent analogue, PY957. We also report the mutagenesis and kinetic analysis of active site mutant proteins at positions 35 and 64 of human (h) DHFR and the crystal structure determinations of hDHFR ternary complexes of NADPH and PY957 with the wild-type DHFR enzyme, the single mutant protein, Gln35Lys, and two double mutant proteins, Gln35Ser/Asn64Ser and Gln35Ser/Asn64Phe. These substitutions place into human DHFR amino acids found at those sites in the opportunistic pathogens pcDHFR (Q35K/N64F) and pjDHFR (Q35S/N64S). The K(i) inhibition constant for PY957 showed greatest potency of the compound for the N64F single mutant protein (5.2 nM), followed by wild-type pcDHFR (K(i) 22 nM) and then wild-type hDHFR enzyme (K(i) 230 nM). Structural data reveal significant conformational changes in the binding interactions of PY957 in the hDHFR Q35S/N64F mutant protein complex compared to the other hDHFR mutant protein complexes and the pcDHFR ternary complex. The conformation of PY957 in the wild-type DHFR is similar to that observed for the single mutant protein. These data support the hypothesis that the enhanced selectivity of PY957 for pcDHFR is in part due to the contributions at positions 37 and 69 (pcDHFR numbering). This insight will help in the design of more selective inhibitors that target these opportunistic pathogens.
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Affiliation(s)
- Vivian Cody
- Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA.
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28
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Volpato JP, Yachnin BJ, Blanchet J, Guerrero V, Poulin L, Fossati E, Berghuis AM, Pelletier JN. Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance. J Biol Chem 2009; 284:20079-89. [PMID: 19478082 PMCID: PMC2740434 DOI: 10.1074/jbc.m109.018010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 05/06/2009] [Indexed: 11/06/2022] Open
Abstract
Methotrexate is a slow, tight-binding, competitive inhibitor of human dihydrofolate reductase (hDHFR), an enzyme that provides key metabolites for nucleotide biosynthesis. In an effort to better characterize ligand binding in drug resistance, we have previously engineered hDHFR variant F31R/Q35E. This variant displays a >650-fold decrease in methotrexate affinity, while maintaining catalytic activity comparable to the native enzyme. To elucidate the molecular basis of decreased methotrexate affinity in the doubly substituted variant, we determined kinetic and inhibitory parameters for the simple variants F31R and Q35E. This demonstrated that the important decrease of methotrexate affinity in variant F31R/Q35E is a result of synergistic effects of the combined substitutions. To better understand the structural cause of this synergy, we obtained the crystal structure of hDHFR variant F31R/Q35E complexed with methotrexate at 1.7-A resolution. The mutated residue Arg-31 was observed in multiple conformers. In addition, seven native active-site residues were observed in more than one conformation, which is not characteristic of the wild-type enzyme. This suggests that increased residue disorder underlies the observed methotrexate resistance. We observe a considerable loss of van der Waals and polar contacts with the p-aminobenzoic acid and glutamate moieties. The multiple conformers of Arg-31 further suggest that the amino acid substitutions may decrease the isomerization step required for tight binding of methotrexate. Molecular docking with folate corroborates this hypothesis.
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Affiliation(s)
| | | | - Jonathan Blanchet
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | - Vanessa Guerrero
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | - Lucie Poulin
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | | | - Albert M. Berghuis
- the Departments of Biochemistry and
- Microbiology and Immunology, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Joelle N. Pelletier
- From the Département de Biochimie and
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
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Mutational 'hot-spots' in mammalian, bacterial and protozoal dihydrofolate reductases associated with antifolate resistance: sequence and structural comparison. Drug Resist Updat 2009; 12:28-41. [PMID: 19272832 DOI: 10.1016/j.drup.2009.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 12/24/2008] [Accepted: 02/04/2009] [Indexed: 12/16/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a primary target for antifolate drugs in cancer treatment, while DHFRs from Plasmodium falciparum, Plasmodium vivax and various bacterial species are primary targets in the treatment of malaria and bacterial infections. Mutations in each of these DHFRs can result in resistance towards clinically relevant antifolates. We review the structural and functional impact of active-site mutations with respect to enzyme activity and antifolate resistance of DHFRs from mammals, protozoa and bacteria. The high structural homology between DHFRs results in a number of cross-species, active-site 'hot-spots' for broad-based antifolate resistance. In addition, we identify mutations that confer species-specific resistance, or antifolate-specific resistance. This comparative review of antifolate binding in diverse species provides new insights into the relationship between antifolate design and the development of mutational resistance. It also presents avenues for designing antifolate-resistant mammalian DHFRs as chemoprotective agents.
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Karasulu H, Kantarcı G, Karaca B, Armagan V, Güneri T, Göker E. Determining the cytotoxicity of methotrexate-loaded microemulsion on human breast, ovarian, and prostate carcinoma cell lines: a new modality for an old drug. Drug Dev Res 2009. [DOI: 10.1002/ddr.20283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Fossati E, Volpato JP, Poulin L, Guerrero V, Dugas DA, Pelletier JN. 2-tier bacterial and in vitro selection of active and methotrexate-resistant variants of human dihydrofolate reductase. ACTA ACUST UNITED AC 2008; 13:504-14. [PMID: 18566481 DOI: 10.1177/1087057108318783] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report a rapid and reliable 2-tier selection and screen for detection of activity as well as drug-resistance in mutated variants of a clinically-relevant drug-target enzyme. Human dihydrofolate reductase point-mutant libraries were subjected to a 1st-tier bacterial complementation assay, such that bacterial propagation served as an indicator of enzyme activity. Alternatively, when selection was performed in the presence of the inhibitor methotrexate (MTX), propagation indicated MTX resistance. The selected variants were then subjected to a 2nd-tier in vitro screen in 96-well plate format using crude bacterial lysate. Conditions were defined to establish a threshold for activity or for MTX resistance. The 2nd-tier assay allowed rapid detection of the best variants among the leads and provided reliable estimates of relative reactivity, (k(cat)) and IC(50)(MTX). Screening saturation libraries of active-site positions 7, 15, 24, 70, and 115 revealed a variety of novel mutations compatible with reactivity as well as 2 novel MTX-resistant variants: V115A and V115C. Both variants displayed K(i)(MTX)=20 nM, a 600-fold increase relative to the wild-type. We also present preliminary results from screening against further antifolates following simple modifications of the protocol. The flexibility and robustness of this method will provide new insights into interactions between ligands and active-site residues of this clinically relevant human enzyme.
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Affiliation(s)
- Elena Fossati
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
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