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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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Akinduti PA, Izevbigie OO, Akinduti OA, Enwose EO, Amoo EO. Fecal Carriage of Colibactin-Encoding Escherichia coli Associated With Colorectal Cancer Among a Student Populace. Open Forum Infect Dis 2024; 11:ofae106. [PMID: 38560611 PMCID: PMC10981395 DOI: 10.1093/ofid/ofae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Fecal carriage of the colibactin (clb) gene in Escherichia coli is described as a source that could promote carcinogenesis, progressing to colorectal cancer. The present study investigated the demographic, dietary, and antibiotic consumption variables as correlates for fecal carriage of clb+/E coli among the student populace. In a randomized cross-sectional survey, E coli (N = 136) from the fecal samples of eligible students were characterized and evaluated for antibiotic resistance, β-lactamase (blm), biofilm, virulence factor production, and strain tryptophan reverse mutagenic activity. The encoded clb+/E coli were analyzed for correlates with principal component analysis. Of all the E coli strains, a low rate of 2 clb+/E coli (1.5%) and higher rates of biofilm (13.2%) and blm producers (11.8%) were recorded among the mutant strains as compared with the nonmutant types. All the clb+/E coli showed complete resistance to amoxicillin, Augmentin (amoxicillin and clavulanate), gentamicin, and trimethoprim/sulfamethoxazole. The fecal clb-encoded E coli (1.5%) were not associated with demographic status, fiber-based food (odds ratio [OR], 1.03; 95% CI, 56.74-138.7; P = .213), alcohol (OR, 1.27; 95% CI, 61.74-147.1; P = .221), antibiotic consumptions (OR, 1.11; 95% CI, 61.29-145.3; P = .222), and handwashing (OR, 1.17; 95% CI, 60.19-145.5; P = .216). The hierarchical cluster of blm+/E coli revealed high-level resistance with a multiantibiotic resistance index ≥0.2 (P < .05). Only 12% of all strains were tryptophan mutant/blm+, and 1.5% of clb+/ECblm+ were observed in fecal samples with a 452-base pair size. Trimethoprim/sulfamethoxazole and biofilm production positively regressed with clb expression (P > .05). Principal component analysis score plot indicated an association of clb+/ECblm+ with dietary pattern, alcohol, blm, and hemolysin production. The combined activity of blm and biofilm production in the gut microbiota could promote clb+/E coli colonization, facilitating genotoxin production and possible colorectal cancer induction.
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Affiliation(s)
- Paul A Akinduti
- Microbiology Unit, Department of Biological Sciences, Covenant University, Ota, Nigeria
| | - Ovbiosa O Izevbigie
- Microbiology Unit, Department of Biological Sciences, Covenant University, Ota, Nigeria
| | | | - Ezekiel O Enwose
- Department of Medical Laboratory Sciences, Neuropsychiatric Hospital, Aro Abeokuta, Nigeria
| | - Emmanuel O Amoo
- Demography and Social Statistics, Covenant University, Ota, Nigeria
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Ramli AH, Mohd Faudzi SM. Diarylpentanoids, the privileged scaffolds in antimalarial and anti-infectives drug discovery: A review. Arch Pharm (Weinheim) 2023; 356:e2300391. [PMID: 37806761 DOI: 10.1002/ardp.202300391] [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: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Asia is a hotspot for infectious diseases, including malaria, dengue fever, tuberculosis, and the pandemic COVID-19. Emerging infectious diseases have taken a heavy toll on public health and the economy and have been recognized as a major cause of morbidity and mortality, particularly in Southeast Asia. Infectious disease control is a major challenge, but many surveillance systems and control strategies have been developed and implemented. These include vector control, combination therapies, vaccine development, and the development of new anti-infectives. Numerous newly discovered agents with pharmacological anti-infective potential are being actively and extensively studied for their bioactivity, toxicity, selectivity, and mode of action, but many molecules lose their efficacy over time due to resistance developments. These facts justify the great importance of the search for new, effective, and safe anti-infectives. Diarylpentanoids, a curcumin derivative, have been developed as an alternative with better bioavailability and metabolism as a therapeutic agent. In this review, the mechanisms of action and potential targets of antimalarial drugs as well as the classes of antimalarial drugs are presented. The bioactivity of diarylpentanoids as a potential scaffold for a new class of anti-infectives and their structure-activity relationships are also discussed in detail.
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Affiliation(s)
- Amirah H Ramli
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti M Mohd Faudzi
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
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4
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Alzahrani HA. Quinoline-2-one derivatives as promising antibacterial agents against multidrug-resistant Gram-positive bacterial strains. Braz J Microbiol 2023; 54:2799-2805. [PMID: 37831330 PMCID: PMC10689604 DOI: 10.1007/s42770-023-01132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023] Open
Abstract
This study describes the discovery of a variety of quinoline2-one derivatives with significant antibacterial action vs a spectrum of multidrug-resistant Gram-positive bacterial strains, especially methicillin-resistant Staphylococcus aureus (MRSA). Compounds 6c, 6l, and 6o exhibited significant antibacterial activity versus the Gram-positive bacterial pathogens evaluated. In comparison to the reference daptomycin, compound 6c demonstrated the most effective activity among the assessed derivatives, with MIC concentrations of 0.75 μg/mL versus MRSA and VRE and 2.50 μg/mL against MRSE. We also reported on these compounds' biofilm and dihydrofolate reductase inhibitory activities. Compound 6c showed the greatest antibiofilm action in a dose-dependent way and a substantial decrease of biofilm development in the MRSA ACL51 strain at concentrations of 0.5, 0.25, and 0.12 MIC, with reductions of 79%, 55%, and 38%, consecutively, whereas the corresponding values for vancomycin were 20%, 12%, and 9%. These findings imply that these quinoline compounds could be used to develop a new category of antibiotic representatives to prevent Gram-positive drug-resistant bacterial strains.
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Affiliation(s)
- Hayat Ali Alzahrani
- Medical Laboratory Technology Department, Applied Medical Science College, Northern Border University, Arar, Saudi Arabia.
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5
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Bui CV, Boswell CW, Ciruna B, Rocheleau JV. Apollo-NADP + reveals in vivo adaptation of NADPH/NADP + metabolism in electrically activated pancreatic β cells. SCIENCE ADVANCES 2023; 9:eadi8317. [PMID: 37792934 PMCID: PMC10550227 DOI: 10.1126/sciadv.adi8317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Several genetically encoded sensors have been developed to study live cell NADPH/NADP+ dynamics, but their use has been predominantly in vitro. Here, we developed an in vivo assay using the Apollo-NADP+ sensor and microfluidic devices to measure endogenous NADPH/NADP+ dynamics in the pancreatic β cells of live zebrafish embryos. Flux through the pentose phosphate pathway, the main source of NADPH in many cell types, has been reported to be low in β cells. Thus, it is unclear how these cells compensate to meet NADPH demands. Using our assay, we show that pyruvate cycling is the main source of NADP+ reduction in β cells, with contributions from folate cycling after acute electrical activation. INS1E β cells also showed a stress-induced increase in folate cycling and further suggested that this cycling requires both increased glycolytic intermediates and cytosolic NAD+. Overall, we show in vivo application of the Apollo-NADP+ sensor and reveal that β cells are capable of adapting NADPH/NADP+ redox during stress.
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Affiliation(s)
- Cindy V. Bui
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Curtis W. Boswell
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Brian Ciruna
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan V. Rocheleau
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
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6
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Cetin E, Guclu TF, Kantarcioglu I, Gaszek IK, Toprak E, Atilgan AR, Dedeoglu B, Atilgan C. Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. J Chem Inf Model 2023; 63:4839-4849. [PMID: 37491825 PMCID: PMC10428214 DOI: 10.1021/acs.jcim.3c00818] [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: 05/29/2023] [Indexed: 07/27/2023]
Abstract
Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR's crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4'-deoxy methyl trimethoprim (4'-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP). To elucidate the inhibition mechanism of 4'-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4'-DTMP is the same, pointing the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site and then on the whole enzyme. We confirmed that the polar modification in 4'-DTMP induces additional local interactions with the enzyme, particularly, the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of inhibitor-bound DHFR must be avoided by a successful inhibitor.
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Affiliation(s)
- Ebru Cetin
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Tandac F. Guclu
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Isik Kantarcioglu
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Ilona K. Gaszek
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Erdal Toprak
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Ali Rana Atilgan
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Burcu Dedeoglu
- Department
of Chemistry, Gebze Technical University, Gebze 41400, Kocaeli, Turkey
| | - Canan Atilgan
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
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Sreelatha S, Nagarajan U, Natarajan S. Protein targets in Mycobacterium tuberculosis and their inhibitors for therapeutic implications: A narrative review. Int J Biol Macromol 2023:125022. [PMID: 37244342 DOI: 10.1016/j.ijbiomac.2023.125022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancement in the area of anti-tubercular drug development has been full-fledged, yet, a very less number of drug molecules have reached phase II clinical trials, and therefore "End-TB" is still a global challenge. Inhibitors to specific metabolic pathways of Mycobacterium tuberculosis (Mtb) gain importance in strategizing anti-tuberculosis drug discovery. The lead compounds that target DNA replication, protein synthesis, cell wall biosynthesis, bacterial virulence and energy metabolism are emerging as potential chemotherapeutic options against Mtb growth and survival within the host. In recent times, the in silico approaches have become most promising tools in the identification of suitable inhibitors for specific protein targets of Mtb. An update in the fundamental understanding of these inhibitors and the mechanism of interaction may bring hope to future perspectives in novel drug development and delivery approaches. This review provides a collective impression of the small molecules with potential antimycobacterial activities and their target pathways in Mtb such as cell wall biosynthesis, DNA replication, transcription and translation, efflux pumps, antivirulence pathways and general metabolism. The mechanism of interaction of specific inhibitor with their respective protein targets has been discussed. The comprehensive knowledge of such an impactful area of research would essentially reflect in the discovery of novel drug molecules and effective delivery approaches. This narrative review encompasses the knowledge of emerging targets and promising n that could potentially translate in to the anti-TB-drug discovery.
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Affiliation(s)
- Souparnika Sreelatha
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Usharani Nagarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Saravanan Natarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India.
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Marrakkur V, Sarojini B, Madar M, Dhanur SH, Sridhara T, Raj CGD, Pavankumar H, Savanur HM, Shetty VR, Naik L. Computational and Experimental Investigation on Biological and Photophysical Properties of High Yielded Novel Aryl-Substituted Pyrazolone Analogue. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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A computational chemistry-driven hypothesis on the mode of action of Hipposudoric Acid and related analogs. Future Med Chem 2022; 14:1115-1131. [PMID: 35796603 DOI: 10.4155/fmc-2022-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: To elucidate the mode of action of the hipposudoric acid derivatives and identify hit compounds for synthesis. Materials & methods: Structural fragments of known bioactive fluorenes were introduced onto the hipposudoric acid scaffold to yield novel derivatives. The binding motifs of the novel compounds were compared to the pharmacophore of DHFR co-crystallized with Methotrexate (MTX). Results: Several of the novel compounds showed binding affinities that exceeded the affinity of the docked endogenous ligand (dihydrofolic acid). Conclusion: This study indicates that compounds 3r12, 3r9, 1s9 and 3r10 are promising candidates for synthesis and pharmacological evaluation.
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Abdallah HY, Ibrahim ME, Abd El-Fadeal NM, Ali DA, Elsehrawy GG, Badr RE, Hassoba HM. Pharmacogenomics of Methotrexate Pathway in Rheumatoid Arthritis Patients: Approach toward Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12071560. [PMID: 35885466 PMCID: PMC9325258 DOI: 10.3390/diagnostics12071560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Methotrexate (MTX) is one of the most common medications used for rheumatoid arthritis (RA) treatment. Single-nucleotide polymorphisms (SNPs) could potentially predict variability in therapeutic outcomes. Aim: This study aims to assess the impact of SNPs in genes encoding for the MTX pathway for predicting clinical and therapeutic responses to MTX in a cohort of Egyptian patients with RA. Subjects and Methods: Data from 107 Egyptian RA patients (aged 44.4 ± 11.4 years) treated with MTX monotherapy, for a duration of 3.7 ± 3.3 years, were collected. Genotypes of 10 SNPs from four different genes were analyzed using the allelic discrimination PCR technique. Results: The ATIC rs3821353 G/T (p = 0.034) and the C/T and C/C of SLC19A1 rs7279445 (p = 0.0018) were associated with a non-response to MTX, while DHFR rs10072026 C/T and C/C were associated with a good response (p < 0.001). Carriers of the ATIC rs382135 3 G (p = 0.001) and ATIC rs4673990 G (p < 0.001) alleles were more likely to develop RA, while the SLC19A1 rs11702425 T (p < 0.001) and GGH rs12681874 T (p = 0.003) allele carriers were more likely to be protected against RA. Carriers of the ATIC rs4673990 A/G genotype (p < 0.001) were at risk of developing RA, while carriers of the following genotypes were mostly protected against RA: ATIC rs3821353 T/T (p < 0.001), ATIC rs3821353 G/G (p = 0.004), SLC19A1 rs11702425 T/T (p = 0.001), SLC19A1 rs11702425 C/T (p = 0.003), GGH rs12681874 C/T (p = 0.004) and GGH rs12681874 T/T (0.002). Conclusion: The genotyping of genes involved in the MTX pathway may be helpful to predict which RA patients will/will not benefit from MTX, and thus, may help to apply a personalized medicine approach in RA.
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Affiliation(s)
- Hoda Y. Abdallah
- Medical Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
| | - Maha E. Ibrahim
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (M.E.I.); (G.G.E.)
| | - Noha M. Abd El-Fadeal
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
- Department of Medical Biochemistry & Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Oncology Diagnostic Unit, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Dina A. Ali
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
- Department of Clinical Pharmacology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Gehad G. Elsehrawy
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (M.E.I.); (G.G.E.)
| | - Rasha E. Badr
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Port Said University, Port Said 42526, Egypt;
| | - Howayda M. Hassoba
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: or ; Tel.: +(2)-01-272-430-312; Fax: +(2)-06-432-16496
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Joshi T, Sharma P, Joshi T, Mathpal S, Pande V, Chandra S. Repurposing of FDA approved drugs against Salmonella enteric serovar Typhi by targeting dihydrofolate reductase: an in silico study. J Biomol Struct Dyn 2022; 40:3731-3744. [PMID: 33251976 DOI: 10.1080/07391102.2020.1850356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
Drug-resistant Salmonella enteric serovar Typhi (S. Typhi) poses a vital public health issue. To overcome drug resistance issues, the development of effective drugs with novel mechanism(s) of action is required. In this regard, drug repurposing is a viable alternative approach to find novel drugs to overcome drug resistance. Therefore, a FDA-approved-drug-library containing 1930 drugs was analyzed against the dihydrofolate reductase (DHFR) of S. Typhi using deep learning regression algorithms. Initially, a total of 500 compounds were screened, followed by rescreening by molecular docking. Further, from screened compounds by molecular docking, the top eight compounds were subjected to molecular dynamics (MD) simulation. Analysis of MD simulation resulted in four potential compounds, namely; Duvelisib, Amenamevir, Lifitegrast and Nilotinib against the DHFR enzyme. During the MD simulation, these four drugs achieved good stability during the 100 ns trajectory period at 300 K. Further to know the insights of the complex's stability, we calculated RMSF, RG, SASA and interaction energy for the last 60 ns trajectory period because all complexes showed the stability after 40 ns trajectory period. MM-PBSA analysis of the last 10 ns of MD trajectories showed the stability of the complexes. From our results, we conclude that these drugs can also be useful for treating typhoid fever and can inhibit S. Typhi by interfering with the function of the DHFR enzyme. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, DSB Campus, Nainital, Uttarakhand, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
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12
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Sazali Hamzah A, Fazli Mohammat M, Wibowo A, Shaameri Z, Nur Ain Abdul Rashid F, Hidayah Pungot N. Five-Membered Nitrogen Heterocycles as New Lead Compounds in Drug Discovery. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Wang Y, Li Y, Liu Y, Zhang Y, Ke Z, Zhang Y, Liu Y. Patients With IBD Receiving Methotrexate Are at Higher Risk of Liver Injury Compared With Patients With Non-IBD Diseases: A Meta-Analysis and Systematic Review. Front Med (Lausanne) 2021; 8:774824. [PMID: 34881269 PMCID: PMC8645797 DOI: 10.3389/fmed.2021.774824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/20/2021] [Indexed: 11/24/2022] Open
Abstract
Background: Methotrexate is well-known in treating inflammatory bowel disease (IBD), rheumatoid arthritis (RA), psoriasis (Ps), and psoriatic arthritis (PsA). Several reports have indicated a higher incidence of methotrexate (MTX)-related liver adverse events in patients with IBD. We aim to investigate the risk of liver injury in patients with IBD and those with non-IBD diseases treated with MTX. Methods: We searched PubMed, Embase, and the Cochrane Library for articles that reported liver adverse events in patients with IBD, RA, and Ps/PsA, receiving MTX therapy. Additional articles were obtained by screening the references of recent meta-analysis and reviews. Raw data from included articles were pooled to calculate the cumulative incidence of total liver injury (TLI), MTX discontinuation (MTX-D), and liver fibrosis (LF). RR (relative risk) was calculated to compare the difference between patients with IBD and those with non-IBD diseases. Results: A total of 326 articles with 128,876 patients were included. The patients with IBD had higher incidence of TLI [11.2 vs. 9.2%; relative risk (RR) = 1.22; P = 0.224] and MTX-D (2.6 vs. 1.8%; RR, 1.48; P = 0.089) than patients with non-IBD diseases. Due to the publication bias, trim-and-fill was performed. Afterwards, the patients with IBD showed significantly higher risk of TLI (11.2 vs. 3%; RR = 3.76; p < 0.001), MTX-D (3.3 vs. 0.7%; RR = 5; p < 0.001) and LF (3.1 vs. 0.1%; RR = 38.62; P = 0.001) compared with patients with non-IBD diseases. Conclusion: IBD is associated with a higher risk of MTX-related liver injury. The mechanism of MTX-induced hepatotoxicity might be different in IBD and non-IBD diseases, and needs to be verified in future research.
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Affiliation(s)
- Yang Wang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yimin Li
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, China
| | - Yun Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yifan Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Ziliang Ke
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yu Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
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14
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Chawla P, Teli G, Gill RK, Narang RK. An Insight into Synthetic Strategies and Recent Developments of Dihydrofolate Reductase Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202102555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pooja Chawla
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
- Pooja Chawla Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga 142001 Punjab India
| | - Ghanshyam Teli
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
| | - Rupinder Kaur Gill
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
| | - Raj Kumar Narang
- Department of Pharmaceutics ISF College of Pharmacy Moga Punjab India
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15
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Alam MS, Saleh MA, Mozibullah M, Riham AT, Solayman M, Gan SH. Computational algorithmic and molecular dynamics study of functional and structural impacts of non-synonymous single nucleotide polymorphisms in human DHFR gene. Comput Biol Chem 2021; 95:107587. [PMID: 34710812 DOI: 10.1016/j.compbiolchem.2021.107587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/21/2021] [Accepted: 10/01/2021] [Indexed: 11/26/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a conserved enzyme that is central to folate metabolism and is widely targeted in pathogenic diseases as well as cancers. Although studies have reported the fact that genetic mutations in DHFR leads to a rare autosomal recessive inborn error of folate metabolism and drug resistance, there is a lack of an extensive study on how the deleterious non-synonymous SNPs (nsSNPs) disrupt its phenotypic effects. In this study, we aim at discovering the structural and functional consequences of nsSNPs in DHFR by employing a combined computational approach consisting of ten recently developed in silico tools for identification of damaging nsSNPs and molecular dynamics (MD) simulation for getting deeper insights into the magnitudes of damaging effects. Our study revealed the presence of 12 most deleterious nsSNPs affecting the native phenotypic effects, with three (R71T, G118D, Y122D) identified in the co-factor and ligand binding active sites. MD simulations also suggested that these three SNPs particularly Y122D, alter the overall structural flexibility and dynamics of the native DHFR protein which can provide more understandings into the crucial roles of these mutants in influencing the loss of DHFR function.
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Affiliation(s)
- Md Shahed Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Abu Saleh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Ashik Tanvir Riham
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia
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16
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Ibrahim SA, Fayed EA, Rizk HF, Desouky SE, Ragab A. Hydrazonoyl bromide precursors as DHFR inhibitors for the synthesis of bis-thiazolyl pyrazole derivatives; antimicrobial activities, antibiofilm, and drug combination studies against MRSA. Bioorg Chem 2021; 116:105339. [PMID: 34530234 DOI: 10.1016/j.bioorg.2021.105339] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 01/15/2023]
Abstract
Microbial resistance is a big concern worldwide, making the development of new antimicrobial drugs difficult. The thiazole and pyrazole rings are important heterocyclic compounds utilized to produce a variety of antimicrobial medications. As a result, a series of new bis-thiazolyl-pyrazole derivatives 3, 4a-c, 5a, b, and 6a-c was synthesized by reacting bis hydrazonoyl bromide with several active methylene reagents in a one-pot reaction. The assigned structure was characterized entirely based on elemental and spectral analyses. The antimicrobial activity represented by MIC was performed using a resazurin-based turbidimetric (TB) assay. The results exhibited good antimicrobial activity against gram-positive strains, especially S. aureus (ATCC6538) while showing poor to moderate activity against gram-negative and fungal strains. Furthermore, the most active derivatives 3, 4a, 4c, and 5b were evaluated for MIC, MBC, antibiofilm, hemolytic assay, and drug combination testing against two S. aureus (ATCC6538) and MRSA (ACL18) strains. Additionally, bis-thiazolyl pyrazole 3, 4c, and 5b exhibited more potent inhibitory activity for DHFR with IC50 values (6.34 ± 0.26, 7.49 ± 0.28, and 3.81 ± 0.16 µM), respectively, compared with Trimethoprim (8.34 ± 0.11 µM). The bis-1-(substituted-thiazol-2-yl)-1H-pyrazole-4-carbonitrile derivative 5b was the most active member with MIC values ranging from (0.12-0.25 µM) compared to Vancomycin (1-2 µM), and MBC values ranging from (0.5-1 µM) for S. aureus (ATCC6538) and MRSA (ACL18). Surprisingly, compound 5b displayed bactericidal behavior, synergistic effect with three commercial antibiotics, and inhibited DHFR with 2.1 folds higher than Trimethoprim. Finally, good findings were obtained from in silico investigations incorporating toxicity prediction and molecular docking simulation.
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Affiliation(s)
- Seham A Ibrahim
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Eman A Fayed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
| | - Hala F Rizk
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Said E Desouky
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ahmed Ragab
- Chemistry Department, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo 11884, Egypt.
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17
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Kou L, Wei S, Kou P. Current Progress and Perspectives on Using Gold Compounds for the Modulation of Tumor Cell Metabolism. Front Chem 2021; 9:733463. [PMID: 34434922 PMCID: PMC8382570 DOI: 10.3389/fchem.2021.733463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 01/14/2023] Open
Abstract
Altered cellular metabolism, which is essential for the growth and survival of tumor cells in a specific microenvironment, is one of the hallmarks of cancer. Among the most significant changes in the metabolic pattern of tumor cells is the shift from oxidative phosphorylation to aerobic glycolysis for glucose utilization. Tumor cells also exhibit changes in patterns of protein and nucleic acid metabolism. Recently, gold compounds have been shown to target several metabolic pathways and a number of metabolites in tumor cells. In this review, we summarize how gold compounds modulate glucose, protein, and nucleic acid metabolism in tumor cells, resulting in anti-tumor effects. We also discuss the rationale underlying the anti-tumor effects of these gold compounds and highlight how to effectively utilize against various types of tumors.
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Affiliation(s)
- Leiya Kou
- The First Clinical College, Hubei University of Chinese Medicine, Wuhan, China
| | - Shuang Wei
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
| | - Pei Kou
- The First Clinical College, Hubei University of Chinese Medicine, Wuhan, China.,Department of Medical Record, Wuhan No. 1 Hospital, Wuhan, China
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18
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Jiang J, Peng L, Wang K, Huang C. Moonlighting Metabolic Enzymes in Cancer: New Perspectives on the Redox Code. Antioxid Redox Signal 2021; 34:979-1003. [PMID: 32631077 DOI: 10.1089/ars.2020.8123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Significance: Metabolic reprogramming is considered to be a critical adaptive biological event that fulfills the energy and biomass demands for cancer cells. One hallmark of metabolic reprogramming is reduced oxidative phosphorylation and enhanced aerobic glycolysis. Such metabolic abnormalities contribute to the accumulation of reactive oxygen species (ROS), the by-products of metabolic pathways. Emerging evidence suggests that ROS can in turn directly or indirectly affect the expression, activity, or subcellular localization of metabolic enzymes, contributing to the moonlighting functions outside of their primary roles. This review summarizes the multifunctions of metabolic enzymes and the involved redox modification patterns, which further reveal the inherent connection between metabolism and cellular redox state. Recent Advances: These noncanonical functions of metabolic enzymes involve the regulation of epigenetic modifications, gene transcription, post-translational modification, cellular antioxidant capacity, and many other fundamental cellular events. The multifunctional properties of metabolic enzymes further expand the metabolic dependencies of cancer cells, and confer cancer cells with a means of adapting to diverse environmental stimuli. Critical Issues: Deciphering the redox-manipulated mechanisms with specific emphasis on the moonlighting function of metabolic enzymes is important for clarifying the pertinence between metabolism and redox processes. Future Directions: Investigation of the redox-regulated moonlighting functions of metabolic enzymes will shed new lights into the mechanism by which metabolic enzymes gain noncanonical functions, and yield new insights into the development of novel therapeutic strategies for cancer treatment by targeting metabolic-redox abnormalities. Antioxid. Redox Signal. 34, 979-1003.
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Affiliation(s)
- Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, People's Republic of China
| | - Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, People's Republic of China
| | - Kui Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, People's Republic of China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, People's Republic of China
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19
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Joshi T, Pundir H, Chandra S. Deep-learning based repurposing of FDA-approved drugs against Candida albicans dihydrofolate reductase and molecular dynamics study. J Biomol Struct Dyn 2021; 40:8420-8436. [PMID: 33879017 DOI: 10.1080/07391102.2021.1911851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Candida albicans causes the fatal fungal bloodstream infection in humans called Candidiasis. Most of the Candida species are resistant to the antifungals used to treat them. Drug-resistant C. albicans poses very serious public health issues. To overcome this, the development of effective drugs with novel mechanism(s) of action is requisite. Drug repurposing is considered a viable alternative approach to overcome the above issue. In the present study, we have attempted to identify drugs that could target the essential enzyme, dihydrofolate reductase of C. albicans (CaDHFR) to find out potent and selective antifungal antifolates. FDA-approved-drug-library from the Selleck database containing 1930 drugs was screened against CaDHFR using deep-learning, molecular docking, X-score and similarity search methods. The screened compounds showing better binding with CaDHFR were subjected to molecular dynamics simulation (MDS). The results of post-MDS analysis like RMSD, RMSF, RG, SASA, the number of hydrogen bonds and PCA suggest that Paritaprevir, Lumacaftor and Rifampin can make good interaction with CaDHFR. Furthermore, analysis of binding free energy corroborated the stability of interactions as they had binding energy of -114.91 kJ mol-1, -79.22 kJ mol-1 and -78.52 kJ mol-1 for Paritaprevir, Lumacaftor and Rifampin respectively as compared to the reference (-63.10 kJ mol-1). From the results, we conclude that these drugs have great potential to inhibit CaDHFR and would add to the drug discovery against candidiasis, and hence these drugs for repurposing should be explored further.
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Affiliation(s)
- Tanuja Joshi
- Department of Botany, Kumaun University, S.S.J. Campus, Almora, Uttarakhand, India
| | - Hemlata Pundir
- Department of Botany, Kumaun University, D.S.B. Campus, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, S.S.J. Campus, Almora, Uttarakhand, India
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20
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Targeting nutrient metabolism with FDA-approved drugs for cancer chemoprevention: Drugs and mechanisms. Cancer Lett 2021; 510:1-12. [PMID: 33857528 DOI: 10.1016/j.canlet.2021.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 12/14/2022]
Abstract
Proliferating cancer cells exhibit metabolic alterations and specific nutritional needs for adapting to their rapid growth. These changes include using aerobic glycolysis, lipid metabolic disorder, and irregular protein degradation. It may be useful to target metabolic abnormalities for cancer chemoprevention. Epidemiological and mechanism-related studies have indicated that many FDA-approved anti-metabolic drugs decrease tumor risk, inhibit tumor growth, or enhance the effect of chemotherapeutic drugs. Drugs targeting nutrient metabolism have fewer side effects with long-term use compared to chemotherapeutic drugs. The characteristics of these drugs make them promising candidates for cancer chemoprevention. Here, we summarize recent discoveries of the chemo-preventive effects of drugs targeting nutrient metabolic pathways and discuss future applications and challenges. Understanding the effects and mechanisms of anti-metabolic drugs in cancer has important implications for exploring strategies for cancer chemoprevention.
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21
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Wróbel A, Drozdowska D. Recent Design and Structure-Activity Relationship Studies on the Modifications of DHFR Inhibitors as Anticancer Agents. Curr Med Chem 2021; 28:910-939. [PMID: 31622199 DOI: 10.2174/0929867326666191016151018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dihydrofolate reductase (DHFR) has been known for decades as a molecular target for antibacterial, antifungal and anti-malarial treatments. This enzyme is becoming increasingly important in the design of new anticancer drugs, which is confirmed by numerous studies including modelling, synthesis and in vitro biological research. This review aims to present and discuss some remarkable recent advances in the research of new DHFR inhibitors with potential anticancer activity. METHODS The scientific literature of the last decade on the different types of DHFR inhibitors has been searched. The studies on design, synthesis and investigation structure-activity relationships were summarized and divided into several subsections depending on the leading molecule and its structural modification. Various methods of synthesis, potential anticancer activity and possible practical applications as DHFR inhibitors of new chemical compounds were described and discussed. RESULTS This review presents the current state of knowledge on the modification of known DHFR inhibitors and the structures and searches for about eighty new molecules, designed as potential anticancer drugs. In addition, DHFR inhibitors acting on thymidylate synthase (TS), carbon anhydrase (CA) and even DNA-binding are presented in this paper. CONCLUSION Thorough physicochemical characterization and biological investigations highlight the structure-activity relationship of DHFR inhibitors. This will enable even better design and synthesis of active compounds, which would have the expected mechanism of action and the desired activity.
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Affiliation(s)
- Agnieszka Wróbel
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
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22
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Škrlj B, Novak MP, Brader G, Anžič B, Ramšak Ž, Gruden K, Kralj J, Kladnik A, Lavrač N, Roitsch T, Dermastia M. New Cross-Talks between Pathways Involved in Grapevine Infection with ' Candidatus Phytoplasma solani' Revealed by Temporal Network Modelling. PLANTS 2021; 10:plants10040646. [PMID: 33805409 PMCID: PMC8065506 DOI: 10.3390/plants10040646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022]
Abstract
Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with ‘Candidatus Phytoplasma solani’, and is one of the most widespread phytoplasma diseases of grapevine in Europe. We proposed a methodology that explores the temporal network dynamics at the community level, i.e., densely connected subnetworks. The methodology offers both insights into the functional dynamics via enrichment analysis at the community level, and analyses of the community dissipation, as a measure that accounts for community degradation. We validated this methodology with cases on experimental temporal expression data of uninfected grapevines and grapevines infected with ‘Ca. P. solani’. These data confirm some known gene communities involved in this infection. They also reveal several new gene communities and their potential regulatory networks that have not been linked to ‘Ca. P. solani’ to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated.
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Affiliation(s)
- Blaž Škrlj
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia;
- Correspondence:
| | - Maruša Pompe Novak
- National Institute of Biology, 1000 Ljubljana, Slovenia; (M.P.N.); (B.A.); (Ž.R.); (K.G.); (M.D.)
- School of Viticulture and Enology, University of Nova Gorica, 5271 Vipava, Slovenia
| | - Günter Brader
- Austrian Institute of Technology, Bioresources Unit, 3430 Tulln, Austria;
| | - Barbara Anžič
- National Institute of Biology, 1000 Ljubljana, Slovenia; (M.P.N.); (B.A.); (Ž.R.); (K.G.); (M.D.)
| | - Živa Ramšak
- National Institute of Biology, 1000 Ljubljana, Slovenia; (M.P.N.); (B.A.); (Ž.R.); (K.G.); (M.D.)
| | - Kristina Gruden
- National Institute of Biology, 1000 Ljubljana, Slovenia; (M.P.N.); (B.A.); (Ž.R.); (K.G.); (M.D.)
| | - Jan Kralj
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia;
| | - Aleš Kladnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Nada Lavrač
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia;
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, 2630 Taastrup, Denmark;
| | - Marina Dermastia
- National Institute of Biology, 1000 Ljubljana, Slovenia; (M.P.N.); (B.A.); (Ž.R.); (K.G.); (M.D.)
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23
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Dhamo B, Jaddoe VWV, Steegers EAP, Wolvius EB, Ongkosuwito EM. The association of maternal folic acid supplementation and prenatal folate and vitamin B12 concentrations with child dental development. Community Dent Oral Epidemiol 2021; 49:445-453. [PMID: 33486813 PMCID: PMC8518742 DOI: 10.1111/cdoe.12620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Low folic acid, folate and vitamin B12 might affect tooth formation and mineralization. The conversion of folic acid into folate is catalysed by the methylenetetrahydrofolate (MTHFR) enzyme which is encoded by the MTHFR gene. Among 3728 mothers and their 10-year-old children from the Generation R Study, we investigated associations of maternal folic acid supplementation and prenatal folate and vitamin B12 concentrations with child dental development. Secondly, we checked the modifying effect of MTHFR-C677T polymorphism. METHODS Information on folic acid supplementation was obtained by questionnaires. Concentrations of folate and vitamin B12 were measured from venous samples taken in early pregnancy. Developmental stages of teeth were defined by the Demirjian method at the age-10 assessment. In addition, dental age of the children was calculated using the Dutch standard. GLM and multivariate linear regression models were built to study the associations. RESULTS Folic acid supplementation started when pregnancy was known (β = -0.09; 95% CI: -0.17, -0.01) and folic acid supplementation started prior to known pregnancy (β = -0.12; 95% CI: -0.20, -0.04) were both associated with decelerated dental development by 1-2 months lower dental age of 10-year-old children. Folate (β = -0.02, 95% CI: -0.05, 0.02) and vitamin B12 (β = 0.03, 95% CI: -0.00, 0.06) were not associated with dental age. MTHFR-C677T did not modify the associations. CONCLUSIONS Maternal folic acid supplementation delays dental development of children by 1-2 months dental age, whereas maternal folate and vitamin B12 concentrations in early pregnancy do not affect the timing of child dental development.
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Affiliation(s)
- Brunilda Dhamo
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Eric A P Steegers
- The Generation R Study Group, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Department of Obstetrics & Gynecology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Eppo B Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Edwin M Ongkosuwito
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, Rotterdam, The Netherlands
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24
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Geijsen AJMR, Ulvik A, Gigic B, Kok DE, van Duijnhoven FJB, Holowatyj AN, Brezina S, van Roekel EH, Baierl A, Bergmann MM, Böhm J, Bours MJL, Brenner H, Breukink SO, Bronner MP, Chang-Claude J, de Wilt JHW, Grady WM, Grünberger T, Gumpenberger T, Herpel E, Hoffmeister M, Huang LC, Jedrzkiewicz JD, Keulen ETP, Kiblawi R, Kölsch T, Koole JL, Kosma K, Kouwenhoven EA, Kruyt FM, Kvalheim G, Li CI, Lin T, Ose J, Pickron TB, Scaife CL, Schirmacher P, Schneider MA, Schrotz-King P, Singer MC, Swanson ER, van Duijvendijk P, van Halteren HK, van Zutphen M, Vickers K, Vogelaar FJ, Wesselink E, Habermann N, Ulrich AB, Ueland PM, Weijenberg MP, Gsur A, Ulrich CM, Kampman E. Circulating Folate and Folic Acid Concentrations: Associations With Colorectal Cancer Recurrence and Survival. JNCI Cancer Spectr 2020; 4:pkaa051. [PMID: 33134831 PMCID: PMC7583160 DOI: 10.1093/jncics/pkaa051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/30/2020] [Accepted: 06/03/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Folates, including folic acid, may play a dual role in colorectal cancer development. Folate is suggested to be protective in early carcinogenesis but could accelerate growth of premalignant lesions or micrometastases. Whether circulating concentrations of folate and folic acid, measured around time of diagnosis, are associated with recurrence and survival in colorectal cancer patients is largely unknown. METHODS Circulating concentrations of folate, folic acid, and folate catabolites p-aminobenzoylglutamate and p-acetamidobenzoylglutamate were measured by liquid chromatography-tandem mass spectrometry at diagnosis in 2024 stage I-III colorectal cancer patients from European and US patient cohort studies. Multivariable-adjusted Cox proportional hazard models were used to assess associations between folate, folic acid, and folate catabolites concentrations with recurrence, overall survival, and disease-free survival. RESULTS No statistically significant associations were observed between folate, p-aminobenzoylglutamate, and p-acetamidobenzoylglutamate concentrations and recurrence, overall survival, and disease-free survival, with hazard ratios ranging from 0.92 to 1.16. The detection of folic acid in the circulation (yes or no) was not associated with any outcome. However, among patients with detectable folic acid concentrations (n = 296), a higher risk of recurrence was observed for each twofold increase in folic acid (hazard ratio = 1.31, 95% confidence interval = 1.02 to 1.58). No statistically significant associations were found between folic acid concentrations and overall and disease-free survival. CONCLUSIONS Circulating folate and folate catabolite concentrations at colorectal cancer diagnosis were not associated with recurrence and survival. However, caution is warranted for high blood concentrations of folic acid because they may increase the risk of colorectal cancer recurrence.
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Affiliation(s)
- Anne J M R Geijsen
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Biljana Gigic
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Andreana N Holowatyj
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Stefanie Brezina
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Eline H van Roekel
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | | | - Jürgen Böhm
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Martijn J L Bours
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Hermann Brenner
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stéphanie O Breukink
- Department of Surgery, GROW School for Oncology and Development Biology, Maastricht University, Maastricht, the Netherlands
| | - Mary P Bronner
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Johannes H W de Wilt
- Department of Surgery, Division of Surgical Oncology and Gastrointestinal Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Tanja Gumpenberger
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Esther Herpel
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lyen C Huang
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | - Eric T P Keulen
- Department of Internal Medicine and Gastroenterology, Zuyderland Medical Center, Sittard, the Netherlands
| | - Rama Kiblawi
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
- Medical Faculty, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Torsten Kölsch
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Janna L Koole
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Katharina Kosma
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Flip M Kruyt
- Department of Surgery, Hospital Gelderse Vallei, Ede, the Netherlands
| | | | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tengda Lin
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Jennifer Ose
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | | | | | | | - Martin A Schneider
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Marie C Singer
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric R Swanson
- Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | | | - Henk K van Halteren
- Department of Internal Medicine, Admiraal de Ruyter Hospital, Goes, the Netherlands
| | - Moniek van Zutphen
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Kathy Vickers
- Department of Surgery, Hospital Gelderse Vallei, Ede, the Netherlands
| | - F Jeroen Vogelaar
- Department of Surgery, VieCuri Medical Center, Venlo, the Netherlands
| | - Evertine Wesselink
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Nina Habermann
- Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alexis B Ulrich
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Matty P Weijenberg
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Andrea Gsur
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
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25
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Gene Expression Signature of Acquired Chemoresistance in Neuroblastoma Cells. Int J Mol Sci 2020; 21:ijms21186811. [PMID: 32948088 PMCID: PMC7555742 DOI: 10.3390/ijms21186811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 01/14/2023] Open
Abstract
Drug resistance of childhood cancer neuroblastoma is a serious clinical problem. Patients with relapsed disease have a poor prognosis despite intense treatment. In the present study, we aimed to identify chemoresistance gene expression signatures in vincristine resistant neuroblastoma cells. We found that vincristine-resistant neuroblastoma cells formed larger clones and survived under reduced serum conditions as compared with non-resistant parental cells. To identify the possible mechanisms underlying vincristine resistance in neuroblastoma cells, we investigated the expression profiles of genes known to be involved in cancer drug resistance. This specific gene expression patterns could predict the behavior of a tumor in response to chemotherapy and for predicting the prognosis of high-risk neuroblastoma patients. Our signature could help chemoresistant neuroblastoma patients in avoiding useless and harmful chemotherapy cycles.
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26
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Sharma K, Neshat N, Sharma S, Giri N, Srivastava A, Almalki F, Saifullah K, Alam MM, Shaquiquzzaman M, Akhter M. Identification of novel selective Mtb-DHFR inhibitors as antitubercular agents through structure-based computational techniques. Arch Pharm (Weinheim) 2019; 353:e1900287. [PMID: 31867798 DOI: 10.1002/ardp.201900287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/01/2019] [Accepted: 12/08/2019] [Indexed: 12/23/2022]
Abstract
Inhibition of dihydrofolate reductase from Mycobacterium tuberculosis-dihydrofolate reductase (Mtb-DHFR) has emerged as a promising approach for the treatment of tuberculosis. To identify novel Mtb-DHFR inhibitors, structure-based virtual screening (SBVS) of the Molecular Diversity Preservation International (MolMall) database was performed using Glide against the Mtb-DHFR and h-DHFR enzymes. On the basis of SBVS, receptor fit, drug-like filters, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis, 16 hits were selected and tested for their antitubercular activity against the H37 RV strain of M. tuberculosis. Five compounds showed promising activity with compounds 11436 and 15275 as the most potent hits with IC50 values of 0.65 and 12.51 μM, respectively, against the H37 RV strain of M. tuberculosis. The two compounds were further tested in the Mtb-DHFR and h-DHFR enzymatic assay for selectivity and were found to be three- to eight-fold selective towards Mtb-DHFR over h-DHFR with minimum inhibitory concentration values of 5.50, 73.89 µM and 42.00, 263.00 µM, respectively. In silico simulation studies also supported the stability of the protein-ligand complex formation. The present study demonstrates the successful utilization of in silico SBVS tools for the identification of novel and potential Mtb-DHFR inhibitors and compound 11436 ((2,4-dihydroxyphenyl)(3,4,5-trihydroxyphenyl)methanone) as a potential lead for the development of novel Mtb-DHFR inhibitors.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Nazia Neshat
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Shweta Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Namita Giri
- Department of Pharmaceutical Sciences, Ferris State University, Big Rapids, Michigan
| | - Apeksha Srivastava
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Faisal Almalki
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Khalid Saifullah
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Md Mumtaz Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | | | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India.,Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi, India
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27
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Engevik MA, Morra CN, Röth D, Engevik K, Spinler JK, Devaraj S, Crawford SE, Estes MK, Kalkum M, Versalovic J. Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors. Front Microbiol 2019; 10:2305. [PMID: 31649646 PMCID: PMC6795088 DOI: 10.3389/fmicb.2019.02305] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Microbial metabolites, including B complex vitamins contribute to diverse aspects of human health. Folate, or vitamin B9, refers to a broad category of biomolecules that include pterin, para-aminobenzoic acid (pABA), and glutamate subunits. Folates are required for DNA synthesis and epigenetic regulation. In addition to dietary nutrients, the gut microbiota has been recognized as a source of B complex vitamins, including folate. This study evaluated the predicted folate synthesis capabilities in the genomes of human commensal microbes identified in the Human Microbiome Project and folate production by representative strains of six human intestinal bacterial phyla. Bacterial folate synthesis genes were ubiquitous across 512 gastrointestinal reference genomes with 13% of the genomes containing all genes required for complete de novo folate synthesis. An additional 39% of the genomes had the genetic capacity to synthesize folates in the presence of pABA, an upstream intermediate that can be obtained through diet or from other intestinal microbes. Bacterial folate synthesis was assessed during exponential and stationary phase growth through the evaluation of expression of select folate synthesis genes, quantification of total folate production, and analysis of folate polyglutamylation. Increased expression of key folate synthesis genes was apparent in exponential phase, and increased folate polyglutamylation occurred during late stationary phase. Of the folate producers, we focused on the commensal Lactobacillus reuteri to examine host-microbe interactions in relation to folate and examined folate receptors in the physiologically relevant human enteroid model. RNAseq data revealed segment-specific folate receptor distribution. Treatment of human colonoid monolayers with conditioned media (CM) from wild-type L. reuteri did not influence the expression of key folate transporters proton-coupled folate transporter (PCFT) or reduced folate carrier (RFC). However, CM from L. reuteri containing a site-specific inactivation of the folC gene, which prevents the bacteria from synthesizing a polyglutamate tail on folate, significantly upregulated RFC expression. No effects were observed using L. reuteri with a site inactivation of folC2, which results in no folate production. This work sheds light on the contributions of microbial folate to overall folate status and mammalian host metabolism.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Christina N. Morra
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Röth
- Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Kristen Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Jennifer K. Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Sridevi Devaraj
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Department of Medicine – Gastroenterology, Hepatology and Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, United States
- Mass Spectrometry and Proteomics Core, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
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28
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Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors. J Antibiot (Tokyo) 2019; 73:5-27. [PMID: 31578455 PMCID: PMC7102388 DOI: 10.1038/s41429-019-0240-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 12/17/2022]
Abstract
The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.
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29
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Rana RM, Rampogu S, Zeb A, Son M, Park C, Lee G, Yoon S, Baek A, Parameswaran S, Park SJ, Lee KW. In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics. J Clin Med 2019; 8:jcm8020233. [PMID: 30754680 PMCID: PMC6406960 DOI: 10.3390/jcm8020233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 01/10/2023] Open
Abstract
Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes thereduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of humanDHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cellproliferation. In the current study, ligand-based pharmacophore modeling identified and evaluatedthe critical chemical features of hDHFR inhibitors. A pharmacophore model (Hypo1) was generatedfrom known inhibitors of DHFR with a correlation coefficient (0.94), root mean square (RMS)deviation (0.99), and total cost value (125.28). Hypo1 was comprised of four chemical features,including two hydrogen bond donors (HDB), one hydrogen bond acceptor (HBA), and onehydrophobic (HYP). Hypo1 was validated using Fischer's randomization, test set, and decoy setvalidations, employed as a 3D query in a virtual screening at Maybridge, Chembridge, Asinex,National Cancer Institute (NCI), and Zinc databases. Hypo1-retrieved compounds were filtered byan absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment test andLipinski's rule of five, where the drug-like hit compounds were identified. The hit compounds weredocked in the active site of hDHFR and compounds with Goldfitness score was greater than 44.67(docking score for the reference compound), clustering analysis, and hydrogen bond interactionswere identified. Furthermore, molecular dynamics (MD) simulation identified three compounds asthe best inhibitors of hDHFR with the lowest root mean square deviation (1.2 Å to 1.8 Å), hydrogenbond interactions with hDHFR, and low binding free energy (-127 kJ/mol to -178 kJ/mol). Finally,the toxicity prediction by computer (TOPKAT) affirmed the safety of the novel inhibitors of hDHFRin human body. Overall, we recommend novel hit compounds of hDHFR for cancer and rheumatoidarthritis chemotherapeutics.
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Affiliation(s)
- Rabia Mukhtar Rana
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Amir Zeb
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Minky Son
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Chanin Park
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Gihwan Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Sanghwa Yoon
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Ayoung Baek
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Sarvanan Parameswaran
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Seok Ju Park
- Department of Internal Medicine, College of Medicine, Busan Paik Hospital, Inje University,Busan 47392, Korea.
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of NaturalScience (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
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30
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Vejnović D, Milić V, Popović B, Damnjanović T, Maksimović N, Bunjevački V, Krajinović M, Novaković I, Damjanov N, Jekić B. Association of C35T polymorphism in dihydrofolate reductase gene with toxicity of methotrexate in rheumatoid arthritis patients. Expert Opin Drug Metab Toxicol 2019; 15:253-257. [DOI: 10.1080/17425255.2019.1563594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dubravka Vejnović
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Vera Milić
- Institute of Rheumatology, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Branka Popović
- Institute of Human Genetics, Faculty of Dental Medicine, University of Belgrade, Beograd, Serbia
| | - Tatjana Damnjanović
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Nela Maksimović
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Vera Bunjevački
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Maja Krajinović
- Canada Service d’Hématologie-Oncologie, Centre de Recherche, Hôpital Sainte-Justine, Montréal, Quebec, Canada
| | - Ivana Novaković
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Nemanja Damjanov
- Institute of Rheumatology, Faculty of Medicine, University of Belgrade, Beograd, Serbia
| | - Biljana Jekić
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Beograd, Serbia
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31
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The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release. Commun Biol 2018; 1:226. [PMID: 30564747 PMCID: PMC6290769 DOI: 10.1038/s42003-018-0236-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/15/2018] [Indexed: 12/02/2022] Open
Abstract
Dihydrofolate reductase (DHFR) catalyzes the stereospecific reduction of 7,8-dihydrofolate (FH2) to (6s)-5,6,7,8-tetrahydrofolate (FH4) via hydride transfer from NADPH. The consensus Escherichia coli DHFR mechanism involves conformational changes between closed and occluded states occurring during the rate-limiting product release step. Although the Protein Data Bank (PDB) contains over 250 DHFR structures, the FH4 complex structure responsible for rate-limiting product release is unknown. We report to our knowledge the first crystal structure of an E. coli. DHFR:FH4 complex at 1.03 Å resolution showing distinct stabilizing interactions absent in FH2 or related (6R)-5,10-dideaza-FH4 complexes. We discover the time course of decay of the co-purified endogenous FH4 during crystal growth, with conversion from FH4 to FH2 occurring in 2–3 days. We also determine another occluded complex structure of E. coli DHFR with a slow-onset nanomolar inhibitor that contrasts with the methotrexate complex, suggesting a plausible strategy for designing DHFR antibiotics by targeting FH4 product conformations. Hongnan Cao et al. present the X-ray crystal structure of E. coli dihydrofolate reductase (DHFR) in complex with its reduced substrate, (6s)-5,6,7,8-tetrahydrofolate (FH4). This structure provides the first glimpse of the rate-limiting product release step of the DHFR mechanism and suggests a strategy for designing DHFR-targeting antibiotics.
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32
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Corral MG, Haywood J, Stehl LH, Stubbs KA, Murcha MW, Mylne JS. Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:727-742. [PMID: 29876984 DOI: 10.1111/tpj.13983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.
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Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Luca H Stehl
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- Faculty of Biology, The University of Freiburg, Schaenzlestrasse 1, Freiburg, 79104, Germany
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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Giletti A, Vital M, Lorenzo M, Cardozo P, Borelli G, Gabus R, Martínez L, Díaz L, Assar R, Rodriguez MN, Esperón P. Methotrexate pharmacogenetics in Uruguayan adults with hematological malignant diseases. Eur J Pharm Sci 2017; 109:480-485. [DOI: 10.1016/j.ejps.2017.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/02/2017] [Accepted: 09/02/2017] [Indexed: 12/24/2022]
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Chang WN, Chi WY, Kao TT, Tsai JN, Liu W, Liang SS, Chiu CC, Chen BH, Fu TF. The Transgenic Zebrafish Display Fluorescence Reflecting the Expressional Dynamics of Dihydrofolate Reductase. Zebrafish 2017; 14:223-235. [DOI: 10.1089/zeb.2016.1381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wen-Ni Chang
- The Institute of Basic Medical Science, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Yu Chi
- The Institute of Basic Medical Science, National Cheng Kung University, Tainan, Taiwan
| | - Tseng-Ting Kao
- The Institute of Basic Medical Science, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ning Tsai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung, Taiwan
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Wangta Liu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Shin Liang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- The Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Bing-Hung Chen
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- The Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Tzu-Fun Fu
- The Institute of Basic Medical Science, National Cheng Kung University, Tainan, Taiwan
- The Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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Abstract
Targeted protein degradation using the PROTAC technology is emerging as a novel therapeutic method to address diseases driven by the aberrant expression of a disease-causing protein. PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase, thus causing ubiquitination and degradation of the target protein by the proteasome. Like small molecules, PROTAC molecules possess good tissue distribution and the ability to target intracellular proteins. Herein, we highlight the advantages of protein degradation using PROTACs, and provide specific examples where degradation offers therapeutic benefit over classical enzyme inhibition. Foremost, PROTACs can degrade proteins regardless of their function. This includes the currently "undruggable" proteome, which comprises approximately 85% of all human proteins. Other beneficial aspects of protein degradation include the ability to target overexpressed and mutated proteins, as well as the potential to demonstrate prolonged pharmacodynamics effect beyond drug exposure. Lastly, due to their catalytic nature and the pre-requisite ubiquitination step, an exquisitely potent molecules with a high degree of degradation selectivity can be designed. Impressive preclinical in vitro and in vivo PROTAC data have been published, and these data have propelled the development of clinically viable PROTACs. With the molecular weight falling in the 700-1000Da range, the delivery and bioavailability of PROTACs remain the largest hurdles on the way to the clinic. Solving these issues and demonstrating proof of concept clinical data will be the focus of many labs over the next few years.
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Arrested Hematopoiesis and Vascular Relaxation Defects in Mice with a Mutation in Dhfr. Mol Cell Biol 2016; 36:1222-36. [PMID: 26830229 DOI: 10.1128/mcb.01035-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/22/2016] [Indexed: 01/06/2023] Open
Abstract
Dihydrofolate reductase (DHFR) is a critical enzyme in the folate metabolism pathway and also plays a role in regulating nitric oxide (NO) signaling in endothelial cells. Although both coding and noncoding mutations with phenotypic effects have been identified in the human DHFR gene, no mouse model is currently available to study the consequences of perturbing DHFR in vivo In order to identify genes involved in definitive hematopoiesis, we performed a forward genetic screen and produced a mouse line, here referred to as Orana, with a point mutation in the Dhfr locus leading to a Thr136Ala substitution in the DHFR protein. Homozygote Orana mice initiate definitive hematopoiesis, but expansion of progenitors in the fetal liver is compromised, and the animals die between embryonic day 13.5 (E13.5) and E14.5. Heterozygote Orana mice survive to adulthood but have tissue-specific alterations in folate abundance and distribution, perturbed stress erythropoiesis, and impaired endothelium-dependent relaxation of the aorta consistent with the role of DHFR in regulating NO signaling. Orana mice provide insight into the dual roles of DHFR and are a useful model for investigating the role of environmental and dietary factors in the context of vascular defects caused by altered NO signaling.
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Schultz A, Qutub AA. Reconstruction of Tissue-Specific Metabolic Networks Using CORDA. PLoS Comput Biol 2016; 12:e1004808. [PMID: 26942765 PMCID: PMC4778931 DOI: 10.1371/journal.pcbi.1004808] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/13/2016] [Indexed: 01/07/2023] Open
Abstract
Human metabolism involves thousands of reactions and metabolites. To interpret this complexity, computational modeling becomes an essential experimental tool. One of the most popular techniques to study human metabolism as a whole is genome scale modeling. A key challenge to applying genome scale modeling is identifying critical metabolic reactions across diverse human tissues. Here we introduce a novel algorithm called Cost Optimization Reaction Dependency Assessment (CORDA) to build genome scale models in a tissue-specific manner. CORDA performs more efficiently computationally, shows better agreement to experimental data, and displays better model functionality and capacity when compared to previous algorithms. CORDA also returns reaction associations that can greatly assist in any manual curation to be performed following the automated reconstruction process. Using CORDA, we developed a library of 76 healthy and 20 cancer tissue-specific reconstructions. These reconstructions identified which metabolic pathways are shared across diverse human tissues. Moreover, we identified changes in reactions and pathways that are differentially included and present different capacity profiles in cancer compared to healthy tissues, including up-regulation of folate metabolism, the down-regulation of thiamine metabolism, and tight regulation of oxidative phosphorylation.
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Affiliation(s)
- André Schultz
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Amina A. Qutub
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- * E-mail:
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38
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Bradbury R, Jiang WG, Cui YX. The clinical and therapeutic uses of MDM2 and PSMA and their potential interaction in aggressive cancers. Biomark Med 2015; 9:1353-70. [PMID: 26581688 DOI: 10.2217/bmm.15.94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Prostate-specific membrane antigen (PSMA) overexpression is observed in the neovasculature of solid tumors, but not in the vasculature of normal tissues. Increased PSMA expression is positively associated with tumor stage and grade, although its function in cancer remains unclear. Mouse double minute 2 (MDM2) is a negative regulator of the p53 tumor suppressor and is reported to regulate VEGF expression and angiogenesis. Both proteins have been considered as biomarkers and therapeutic targets for advanced solid tumors. Our work and a recent microarray-based gene profiling study suggest there could be signaling interplay between MDM2 and PSMA. We herein review the mechanisms underlining the outgrowth of tumors associated with PSMA and MDM2, their potential interaction and how this may be applied to anticancer therapeutics.
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Affiliation(s)
- Robyn Bradbury
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
| | - Yu-Xin Cui
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
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39
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Phase II trial of carboplatin and pemetrexed as first-line chemotherapy for non-squamous non-small cell lung cancer, and correlation between the efficacy/toxicity and genetic polymorphisms associated with pemetrexed metabolism: Hokkaido Lung Cancer Clinical Study Group Trial (HOT) 0902. Cancer Chemother Pharmacol 2014; 74:1149-57. [DOI: 10.1007/s00280-014-2589-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/08/2014] [Indexed: 01/27/2023]
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40
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Meethal SV, Hogan KJ, Mayanil CS, Iskandar BJ. Folate and epigenetic mechanisms in neural tube development and defects. Childs Nerv Syst 2013; 29:1427-33. [PMID: 24013316 DOI: 10.1007/s00381-013-2162-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Multiple genetic and epigenetic factors involved in central nervous system (CNS) development influence the incidence of neural tube defects (NTDs). DISCUSSION The beneficial effect of periconceptional folic acid on NTD prevention denotes a vital role for the single-carbon biochemical pathway in NTD genesis. Indeed, NTDs are associated with polymorphisms in a diversity of genes that encode folate pathway enzymes. Recent evidence suggests that CNS development and function, and consequently NTDs, are also associated with epigenetic mechanisms, many of which participate in the folate cycle and its input and output pathways. We provide an overview with select examples drawn from the authors' research.
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Affiliation(s)
- Sivan Vadakkadath Meethal
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, WI 53792, USA
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41
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Galbiatti ALS, Castro R, Caldas HC, Padovani JA, Pavarino EC, Goloni-Bertollo EM. Alterations in the expression pattern of MTHFR, DHFR, TYMS, and SLC19A1 genes after treatment of laryngeal cancer cells with high and low doses of methotrexate. Tumour Biol 2013; 34:3765-71. [PMID: 23838799 DOI: 10.1007/s13277-013-0960-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/19/2013] [Indexed: 12/18/2022] Open
Abstract
Inter-individual variations to methotrexate (MTX) outcome have been attributed to different expression profiles of genes related to folate metabolism. To elucidate the mechanisms of variations to MTX outcome, we investigated MTHFR, DHFR, TYMS, and SLC19A1 gene expression profiles by quantifying the mRNA level of the genes involved in folate metabolism to MTX response in laryngeal cancer cell line (HEP-2). For this, three different concentrations of MTX (0.25, 25, and 75 μmol) were added separately in HEP-2 cell line for 24 h at 37 °C. Apoptotis quantification was evaluated with fluorescein isothiocyanate-labeled Bcl-2 by flow cytometry. Real-time quantitative PCR technique was performed by quantification of gene expression with TaqMan® Gene Expression Assay. ANOVA and Bonferroni's post hoc tests were utilized for statistical analysis. The results showed that the numbers of apoptotic HEP-2 cells with 0.25, 25.0, and 75.0 μmol of MTX were 14.57, 77.54, and 91.58%, respectively. We found that the expression levels for MTHFR, DHFR, TYMS, and SLC19A1 genes were increased in cells with 75.0 μmol of MTX (p < 0.05). Moreover, SLC19A1 gene presented lower expression in cells treated with 0.25 μmol of MTX (p < 0.05). In conclusion, our data suggest that MTHFR, DHFR, TYMS, and SLC19A1 genes present increased expression after the highest application of MTX dose in laryngeal cancer cell line. Furthermore, SLC19A1 gene also presents decreased expression after the lowest application of MTX dose in laryngeal cancer cell line. Significant alterations of expression of these studied genes in cell culture model may give support for studies in clinical practice and predict interesting and often novel mechanisms of resistance of MTX chemotherapy.
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Affiliation(s)
- Ana Lívia Silva Galbiatti
- Genetics and Molecular Biology Research Unit (UPGEM), São José do Rio Preto Medical School (FAMERP), Avenida Brigadeiro Faria Lima, n.5416, São José do Rio Preto, SP, Brazil,
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Sasaki S, Watanabe T, Nakayama H. Analysis of the mRNA expression of chemotherapy-related genes in colorectal carcinoma using the danenberg tumor profile method. JOURNAL OF ONCOLOGY 2013; 2013:386906. [PMID: 23577026 PMCID: PMC3612437 DOI: 10.1155/2013/386906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/25/2013] [Indexed: 02/04/2023]
Abstract
The establishment of individualized chemotherapy for colorectal carcinoma based on the expression of genes involved in chemotherapeutic sensitivity or prognosis is necessary. To achieve this, the expression profiles of genes within tumors and their relationship to clinicopathological factors must be elucidated. Here, we selected 10 genes (TS, DPD, TP, FPGS, GGH, DHFR, ERCC1, TOPO-1, VEGF, and EGFR), examined differences in their mRNA expression between the upper and lower thirds of tumors by laser-captured microdissection and real-time RT-PCR (the Danenberg tumor profile), and analyzed the relationships between their expression profiles and clinicopathological factors. Interestingly, the mRNA expression of DPD, TP, and VEGF was significantly higher in the lower third than in the upper third of tumors (P = 0.044, 0.023, and 0.013, resp.). Furthermore, increased ERCC1 mRNA expression in the lower third of tumors correlated with recurrence (P = 0.049), and VEGF mRNA expression was significantly higher in cases with recurrence than in cases without recurrence, both in the upper and lower thirds of tumors (P = 0.018 and 0.036, resp.). These results implied that heterogeneity in DPD, TP, and VEGF expression may exist in colorectal carcinoma and that ERCC-1 and VEGF may be markers predicting recurrence after curative operation.
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Affiliation(s)
- Shin Sasaki
- Department of Surgery, Omori Red Cross Hospital, 4-30-1, Chuo, Ota-ku, Tokyo 143-8527, Japan
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Schaevitz LR, Berger-Sweeney JE. Gene-Environment Interactions and Epigenetic Pathways in Autism: The Importance of One-Carbon Metabolism. ILAR J 2012; 53:322-40. [DOI: 10.1093/ilar.53.3-4.322] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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44
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Vázquez E, Corchero JL, Burgueño JF, Seras-Franzoso J, Kosoy A, Bosser R, Mendoza R, Martínez-Láinez JM, Rinas U, Fernández E, Ruiz-Avila L, García-Fruitós E, Villaverde A. Functional inclusion bodies produced in bacteria as naturally occurring nanopills for advanced cell therapies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:1742-1747. [PMID: 22410789 DOI: 10.1002/adma.201104330] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/25/2011] [Indexed: 05/31/2023]
Abstract
Inclusion bodies (50-500 nm in diameter) produced in recombinant bacteria can be engineered to contain functional proteins with therapeutic potential. Upon exposure, these protein particles are efficiently internalized by mammalian cells and promote recovery from diverse stresses. Being fully biocompatible, inclusion bodies are a novel platform, as tailored nanopills, for sustained drug release in advanced cell therapies.
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Affiliation(s)
- Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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