101
|
Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ. The peroxidation-derived DNA adduct, 6-oxo-M 1dG, is a strong block to replication by human DNA polymerase η. J Biol Chem 2023; 299:105067. [PMID: 37468099 PMCID: PMC10450521 DOI: 10.1016/j.jbc.2023.105067] [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: 03/22/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
The DNA adduct 6-oxo-M1dG, (3-(2'-deoxy-β-D-erythro-pentofuranosyl)-6-oxo-pyrimido(1,2alpha)purin-10(3H)-one) is formed in the genome via oxidation of the peroxidation-derived adduct M1dG. However, the effect of 6-oxo-M1dG adducts on subsequent DNA replication is unclear. Here we investigated the ability of the human Y-family polymerase hPol η to bypass 6-oxo-M1dG. Using steady-state kinetics and analysis of DNA extension products by liquid chromatography-tandem mass spectrometry, we found hPol η preferentially inserts a dAMP or dGMP nucleotide into primer-templates across from the 6-oxo-M1dG adduct, with dGMP being slightly preferred. We also show primer-templates with a 3'-terminal dGMP or dAMP across from 6-oxo-M1dG were extended to a greater degree than primers with a dCMP or dTMP across from the adduct. In addition, we explored the structural basis for bypass of 6-oxo-M1dG by hPol η using X-ray crystallography of both an insertion-stage and an extension-stage complex. In the insertion-stage complex, we observed that the incoming dCTP opposite 6-oxo-M1dG, although present during crystallization, was not present in the active site. We found the adduct does not interact with residues in the hPol η active site but rather forms stacking interactions with the base pair immediately 3' to the adduct. In the extension-stage complex, we observed the 3' hydroxyl group of the primer strand dGMP across from 6-oxo-M1dG is not positioned correctly to form a phosphodiester bond with the incoming dCTP. Taken together, these results indicate 6-oxo-M1dG forms a strong block to DNA replication by hPol η and provide a structural basis for its blocking ability.
Collapse
Affiliation(s)
- Robyn Richie-Jannetta
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Pradeep Pallan
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Philip J Kingsley
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nikhil Kamdar
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lawrence J Marnett
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| |
Collapse
|
102
|
Wang Q, Serda M, Li Q, Sun T. Recent Advancements on Self-Immolative System Based on Dynamic Covalent Bonds for Delivering Heterogeneous Payloads. Adv Healthc Mater 2023; 12:e2300138. [PMID: 36943096 DOI: 10.1002/adhm.202300138] [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: 01/12/2023] [Revised: 03/10/2023] [Indexed: 03/23/2023]
Abstract
The precisely spatial-temporal delivery of heterogeneous payloads from a single system with the same pulse is in great demand in realizing versatile and synergistic functions. Very few molecular architectures can satisfy the strict requirements of dual-release translated from single triggers, while the self-immolative systems based on dynamic covalent bonds represent the "state-of-art" of ultimate solution strategy. Embedding heterogeneous payloads symmetrically onto the self-immolative backbone with dynamic covalent bonds as the trigger, can respond to the quasi-bio-orthogonal hallmarks which are higher at the disease's microenvironment to simultaneously yield the heterogeneous payloads (drug A/drug B or drug/reporter). In this review, the modular design principles are concentrated to illustrate the rules in tailoring useful structures, then the rational applications are enumerated on the aspects of drug codelivery and visualized drug-delivery. This review, hopefully, can give the general readers a comprehensive understanding of the self-immolative systems based on dynamic covalent bonds for delivering heterogeneous payloads.
Collapse
Affiliation(s)
- Qingbing Wang
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, 200025, P. R. China
- Key Laboratory of Smart Drug Delivery Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, P. R. China
| | - Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice, Katowice, 40-006, Poland
| | - Quan Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 10 Boyanghu Road, Tianjin, 301617, P. R. China
- College of Chemistry and Chemical Engineering, Hubei University, 368 Youyidadao Avenue, Wuhan, 430062, P. R. China
| | - Tao Sun
- Key Laboratory of Smart Drug Delivery Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, P. R. China
| |
Collapse
|
103
|
Bainbridge L, Zabrady K, Doherty A. Primase-polymerases: how to make a primer from scratch. Biosci Rep 2023; 43:BSR20221986. [PMID: 37358261 PMCID: PMC10345425 DOI: 10.1042/bsr20221986] [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: 04/04/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 06/27/2023] Open
Abstract
To pass on genetic information to the next generation, cells must faithfully replicate their genomes to provide copies for each daughter cell. To synthesise these duplicates, cells employ specialised enzymes called DNA polymerases, which rapidly and accurately replicate nucleic acid polymers. However, most polymerases lack the ability to directly initiate DNA synthesis and required specialised replicases called primases to make short polynucleotide primers, from which they then extend. Replicative primases (eukaryotes and archaea) belong to a functionally diverse enzyme superfamily known as Primase-Polymerases (Prim-Pols), with orthologues present throughout all domains of life. Characterised by a conserved catalytic Prim-Pol domain, these enzymes have evolved various roles in DNA metabolism, including DNA replication, repair, and damage tolerance. Many of these biological roles are fundamentally underpinned by the ability of Prim-Pols to generate primers de novo. This review examines our current understanding of the catalytic mechanisms utilised by Prim-Pols to initiate primer synthesis.
Collapse
Affiliation(s)
- Lewis J. Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Aidan J. Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| |
Collapse
|
104
|
Mori T, Yoshida N. Tuning the ATP-ATP and ATP-disordered protein interactions in high ATP concentration by altering water models. J Chem Phys 2023; 159:035102. [PMID: 37458354 DOI: 10.1063/5.0158046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
The adenosine triphosphate (ATP)-protein interactions have been of great interest since the recent experimental finding of ATP's role as a hydrotrope. The interaction between ATP and disordered proteins is fundamental to the dissolution of protein aggregates and the regulation of liquid-liquid phase separation by ATP. Molecular dynamics simulation is a powerful tool for analyzing these interactions in molecular detail but often suffers from inaccuracies in describing disordered proteins and ATPs in high concentrations. Recently, several water models have been proposed to improve the description of the protein-disordered states, yet how these models work with ATP has not been explored. To this end, here, we study how water models affect ATP and alter the ATP-ATP and ATP-protein interactions for the intrinsically disordered protein, α-Synuclein. Three water models, TIP4P-D, OPC, and TIP3P, are compared, while the protein force field is fixed to ff99SBildn. The results show that ATP over-aggregates into a single cluster in TIP3P water, but monomers and smaller clusters are found in TIP4P-D and OPC waters. ATP-protein interaction is also over-stabilized in TIP3P, whereas repeated binding/unbinding of ATP to α-Synuclein is observed in OPC and TIP4P-D waters, which is in line with the recent nuclear magnetic resonance experiment. The adenine ring-mediated interaction is found to play a major role in ATP-ATP and ATP-protein contacts. Interestingly, changing Mg2+ into Na+ strengthened the electrostatic interaction and promoted ATP oligomerization and ATP-α-Synuclein binding. Overall, this study shows that changing the water model can be an effective approach to improve the properties of ATP in high concentration.
Collapse
Affiliation(s)
- Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Department of Interdisciplinary Engineering Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| |
Collapse
|
105
|
Wagner AG, Eskandari R, Schramm VL. An enzyme-coupled microplate assay for activity and inhibition of hmdUMP hydrolysis by DNPH1. Anal Biochem 2023; 672:115171. [PMID: 37142196 PMCID: PMC10334339 DOI: 10.1016/j.ab.2023.115171] [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: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
2'-Deoxynucleoside 5'-monophosphate N-glycosidase 1 (DNPH1) hydrolyzes the epigenetically modified nucleotide 5-hydroxymethyl 2'-deoxyuridine 5'-monophosphate (hmdUMP) derived from DNA metabolism. Published assays of DNPH1 activity are low throughput, use high concentrations of DNPH1, and have not incorporated or characterized reactivity with the natural substrate. We describe the enzymatic synthesis of hmdUMP from commercially available materials and define its steady-state kinetics with DNPH1 using a sensitive, two-pathway enzyme coupled assay. This continuous absorbance-based assay works in 96-well plate format using nearly 500-fold less DNPH1 than previous methods. With a Z prime value of 0.92, the assay is suitable for high-throughput assays, screening of DNPH1 inhibitors, or characterization of other deoxynucleotide monophosphate hydrolases.
Collapse
Affiliation(s)
- Andrew G Wagner
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States
| | - Roozbeh Eskandari
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States.
| |
Collapse
|
106
|
Hong KU, Tagnedji AH, Doll MA, Walls KM, Hein DW. Upregulation of cytidine deaminase in NAT1 knockout breast cancer cells. J Cancer Res Clin Oncol 2023; 149:5047-5060. [PMID: 36329350 PMCID: PMC10193532 DOI: 10.1007/s00432-022-04436-w] [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: 08/15/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE Arylamine N-acetyltransferase 1 (NAT1), a phase II metabolic enzyme, is frequently upregulated in breast cancer. Inhibition or depletion of NAT1 leads to growth retardation in breast cancer cells in vitro and in vivo. A previous metabolomics study of MDA-MB-231 breast cancer cells suggests that NAT1 deletion leads to a defect in de novo pyrimidine biosynthesis. In the present study, we observed that NAT1 deletion results in upregulation of cytidine deaminase (CDA), which is involved in the pyrimidine salvage pathway, in multiple breast cancer cell lines (MDA-MB-231, MCF-7 and ZR-75-1). We hypothesized that NAT1 KO MDA-MB-231 cells show differential sensitivity to drugs that either inhibit cellular pyrimidine homeostasis or are metabolized by CDA. METHODS The cells were treated with (1) inhibitors of dihydroorotate dehydrogenase or CDA (e.g., teriflunomide and tetrahydrouridine); (2) pyrimidine/nucleoside analogs (e.g., gemcitabine and 5-azacytidine); and (3) naturally occurring, modified cytidines (e.g., 5-formyl-2'-deoxycytidine; 5fdC). RESULTS Although NAT1 KO cells failed to show differential sensitivity to nucleoside analogs that are metabolized by CDA, they were markedly more sensitive to 5fdC which induces DNA damage in the presence of high CDA activity. Co-treatment with 5fdC and a CDA inhibitor, tetrahydrouridine, abrogated the increase in 5fdC cytotoxicity in NAT1 KO cells, suggesting that the increased sensitivity of NAT1 KO cells to 5fdC is dependent on their increased CDA activity. CONCLUSIONS The present findings suggest a novel therapeutic strategy to treat breast cancer with elevated NAT1 expression. For instance, NAT1 inhibition may be combined with cytotoxic nucleosides (e.g., 5fdC) for breast cancer treatment.
Collapse
Affiliation(s)
- Kyung U Hong
- Department of Pharmacology & Toxicology and Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
| | - Afi H Tagnedji
- Department of Pharmacology & Toxicology and Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mark A Doll
- Department of Pharmacology & Toxicology and Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kennedy M Walls
- Department of Pharmacology & Toxicology and Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - David W Hein
- Department of Pharmacology & Toxicology and Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
| |
Collapse
|
107
|
Yang CH, Wu CH, Lo SY, Lua AC, Chan YR, Li HC. Hepatitis C Virus Down-Regulates the Expression of Ribonucleotide Reductases to Promote Its Replication. Pathogens 2023; 12:892. [PMID: 37513740 PMCID: PMC10383090 DOI: 10.3390/pathogens12070892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Ribonucleotide reductases (RRs or RNRs) catalyze the reduction of the OH group on the 2nd carbon of ribose, reducing four ribonucleotides (NTPs) to the corresponding deoxyribonucleotides (dNTPs) to promote DNA synthesis. Large DNA viruses, such as herpesviruses and poxviruses, could benefit their replication through increasing dNTPs via expression of viral RRs. Little is known regarding the relationship between cellular RRs and RNA viruses. Mammalian RRs contain two subunits of ribonucleotide reductase M1 polypeptide (RRM1) and two subunits of ribonucleotide reductase M2 polypeptide (RRM2). In this study, expression of cellular RRMs, including RRM1 and RRM2, is found to be down-regulated in hepatitis C virus (HCV)-infected Huh7.5 cells and Huh7 cells with HCV subgenomic RNAs (HCVr). As expected, the NTP/dNTP ratio is elevated in HCVr cells. Compared with that of the control Huh7 cells with sh-scramble, the NTP/dNTP ratio of the RRM-knockdown cells is elevated. Knockdown of RRM1 or RRM2 increases HCV replication in HCV replicon cells. Moreover, inhibitors to RRMs, including Didox, Trimidox and hydroxyurea, enhance HCV replication. Among various HCV viral proteins, the NS5A and/or NS3/4A proteins suppress the expression of RRMs. When these are taken together, the results suggest that HCV down-regulates the expression of RRMs in cultured cells to promote its replication.
Collapse
Affiliation(s)
- Chee-Hing Yang
- Department of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Cheng-Hao Wu
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
| | - Shih-Yen Lo
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Department of Laboratory Medicine and Biotechnology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Ahai-Chang Lua
- Department of Laboratory Medicine and Biotechnology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Yu-Ru Chan
- Department of Laboratory Medicine and Biotechnology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| |
Collapse
|
108
|
Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
Collapse
Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| |
Collapse
|
109
|
Takizawa Y, Kizawa M, Niwa N, Komura Y, Takahashi M, Koda D, Kurita T, Nakajima T. Specific inhibitory effects of guanosine on breast cancer cell proliferation. Biochem Biophys Res Commun 2023; 673:67-72. [PMID: 37356147 DOI: 10.1016/j.bbrc.2023.06.069] [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: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
Breast cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death. Drug therapy for breast cancer is currently selected based on the subtype classification; however, many anticancer drugs are highly cytotoxic. Since intracellular levels of GTP are elevated in many cancer cells that undergo a specific cell proliferation cycle, GTP has potential as a target for cancer therapy. The present study focused on nucleosides and nucleotides and examined intracellular GTP-dependent changes in cell proliferation rates in normal (MCF-12A) and cancer (MCF-7) breast cell lines. Decreased cell proliferation due to a reduction in intracellular GTP levels by mycophenolic acid (MPA), an inosine monophosphate dehydrogenase inhibitor, was observed in both cell lines. The inhibitory effects of MPA on cell proliferation were suppressed when it was applied in combination with Guanosine (Guo), a substrate for GTP salvage synthesis, while the single exposure to Guo suppressed the proliferation of MCF-7 cells only. Although the underlying mechanisms remain unclear, since the inhibitory effects of Guo on cell proliferation did not correlate with GTP or ATP intracellular levels or the GTP/ATP ratio, there may be another cause besides GTP metabolism. Guo inhibited the proliferation of MCF-7, a human breast cancer cell line, but not MCF-12A, a human normal breast cell line. Further studies are needed to investigate the potential of applying Guo as a target for the development of a novel cancer treatment system.
Collapse
Affiliation(s)
- Yusuke Takizawa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan.
| | - Masayuki Kizawa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Nobuyuki Niwa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Yuya Komura
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Masato Takahashi
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Daiki Koda
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Takuro Kurita
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Takanori Nakajima
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| |
Collapse
|
110
|
Tong Y, Wu X, Liu Y, Chen H, Zhou Y, Jiang L, Li M, Zhao S, Zhang Y. Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage. Nat Microbiol 2023:10.1038/s41564-023-01410-1. [PMID: 37308591 DOI: 10.1038/s41564-023-01410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.
Collapse
Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| | - Xinying Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Huiyu Chen
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Department of Chemistry, Tianjin University, Tianjin, China.
| |
Collapse
|
111
|
Schneider A, Bergsch J, Lipps G. The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically. Nucleic Acids Res 2023; 51:5087-5105. [PMID: 37099378 PMCID: PMC10250227 DOI: 10.1093/nar/gkad261] [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: 09/13/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/27/2023] Open
Abstract
The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the large regulatory subunits of archaeoeukaryotic heterodimeric primases in one protein chain. The recombinant protein primes on templates containing a triplet with a central thymidine, thus displaying a pronounced sequence specificity typically observed with bacterial type primases only. The N. equitans primase (NEQ395) is a highly active primase enzyme synthesizing short RNA primers. Termination occurs preferentially at about nine nucleotides, as determined by HPLC analysis and confirmed with mass spectrometry. Possibly, the compact monomeric primase NEQ395 represents the minimal archaeoeukaryotic primase and could serve as a functional and structural model of the heterodimeric archaeoeukaryotic primases, whose study is hindered by engagement in protein assemblies and rather low activity.
Collapse
Affiliation(s)
- Andy Schneider
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Jan Bergsch
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| |
Collapse
|
112
|
Flickinger KM, Wilson KM, Rossiter NJ, Hunger AL, Lee TD, Hall MD, Cantor JR. Conditional lethality profiling reveals anticancer mechanisms of action and drug-nutrient interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543621. [PMID: 37333068 PMCID: PMC10274668 DOI: 10.1101/2023.06.04.543621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chemical screening studies have identified drug sensitivities across hundreds of cancer cell lines but most putative therapeutics fail to translate. Discovery and development of drug candidates in models that more accurately reflect nutrient availability in human biofluids may help in addressing this major challenge. Here we performed high-throughput screens in conventional versus Human Plasma-Like Medium (HPLM). Sets of conditional anticancer compounds span phases of clinical development and include non-oncology drugs. Among these, we characterize a unique dual-mechanism of action for brivudine, an agent otherwise approved for antiviral treatment. Using an integrative approach, we find that brivudine affects two independent targets in folate metabolism. We also traced conditional phenotypes for several drugs to the availability of nucleotide salvage pathway substrates and verified others for compounds that seemingly elicit off-target anticancer effects. Our findings establish generalizable strategies for exploiting conditional lethality in HPLM to reveal therapeutic candidates and mechanisms of action.
Collapse
|
113
|
Greiser M, Karbowski M, Kaplan AD, Coleman AK, Verhoeven N, Mannella CA, Lederer WJ, Boyman L. Calcium and bicarbonate signaling pathways have pivotal, resonating roles in matching ATP production to demand. eLife 2023; 12:e84204. [PMID: 37272417 PMCID: PMC10284600 DOI: 10.7554/elife.84204] [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: 10/14/2022] [Accepted: 06/01/2023] [Indexed: 06/06/2023] Open
Abstract
Mitochondrial ATP production in ventricular cardiomyocytes must be continually adjusted to rapidly replenish the ATP consumed by the working heart. Two systems are known to be critical in this regulation: mitochondrial matrix Ca2+ ([Ca2+]m) and blood flow that is tuned by local cardiomyocyte metabolic signaling. However, these two regulatory systems do not fully account for the physiological range of ATP consumption observed. We report here on the identity, location, and signaling cascade of a third regulatory system -- CO2/bicarbonate. CO2 is generated in the mitochondrial matrix as a metabolic waste product of the oxidation of nutrients. It is a lipid soluble gas that rapidly permeates the inner mitochondrial membrane and produces bicarbonate in a reaction accelerated by carbonic anhydrase. The bicarbonate level is tracked physiologically by a bicarbonate-activated soluble adenylyl cyclase (sAC). Using structural Airyscan super-resolution imaging and functional measurements we find that sAC is primarily inside the mitochondria of ventricular cardiomyocytes where it generates cAMP when activated by bicarbonate. Our data strongly suggest that ATP production in these mitochondria is regulated by this cAMP signaling cascade operating within the inter-membrane space by activating local EPAC1 (Exchange Protein directly Activated by cAMP) which turns on Rap1 (Ras-related protein-1). Thus, mitochondrial ATP production is increased by bicarbonate-triggered sAC-signaling through Rap1. Additional evidence is presented indicating that the cAMP signaling itself does not occur directly in the matrix. We also show that this third signaling process involving bicarbonate and sAC activates the mitochondrial ATP production machinery by working independently of, yet in conjunction with, [Ca2+]m-dependent ATP production to meet the energy needs of cellular activity in both health and disease. We propose that the bicarbonate and calcium signaling arms function in a resonant or complementary manner to match mitochondrial ATP production to the full range of energy consumption in ventricular cardiomyocytes.
Collapse
Affiliation(s)
- Maura Greiser
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Physiology, University of Marylan School of MedicineBaltimoreUnited States
- Claude D. Pepper Older Americans Independence Center, University of Maryland School of MedicineBaltimoreUnited States
| | - Mariusz Karbowski
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Biochemistry and Molecular Biology, University of Maryland School of MedicineBaltimoreUnited States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore School of MedicineBaltimoreUnited States
| | - Aaron David Kaplan
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of MedicineBaltimoreUnited States
| | - Andrew Kyle Coleman
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Physiology, University of Marylan School of MedicineBaltimoreUnited States
| | - Nicolas Verhoeven
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Biochemistry and Molecular Biology, University of Maryland School of MedicineBaltimoreUnited States
| | - Carmen A Mannella
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Physiology, University of Marylan School of MedicineBaltimoreUnited States
| | - W Jonathan Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Physiology, University of Marylan School of MedicineBaltimoreUnited States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore School of MedicineBaltimoreUnited States
| | - Liron Boyman
- Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimoreUnited States
- Department of Physiology, University of Marylan School of MedicineBaltimoreUnited States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore School of MedicineBaltimoreUnited States
| |
Collapse
|
114
|
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E. RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell 2023; 186:2425-2437.e21. [PMID: 37196657 PMCID: PMC10515295 DOI: 10.1016/j.cell.2023.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023]
Abstract
Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence demonstrating that ribonucleotide excision repair (RER) is directly coupled to transcription. Affinity pull-downs and mass-spectrometry-assisted mapping of in cellulo inter-protein cross-linking reveal the majority of RNaseHII molecules interacting with RNA polymerase (RNAP) in E. coli. Cryoelectron microscopy structures of RNaseHII bound to RNAP during elongation, with and without the target rNMP substrate, show specific protein-protein interactions that define the transcription-coupled RER (TC-RER) complex in engaged and unengaged states. The weakening of RNAP-RNaseHII interactions compromises RER in vivo. The structure-functional data support a model where RNaseHII scans DNA in one dimension in search for rNMPs while "riding" the RNAP. We further demonstrate that TC-RER accounts for a significant fraction of repair events, thereby establishing RNAP as a surveillance "vehicle" for detecting the most frequently occurring replication errors.
Collapse
Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
115
|
Ahn D, Provasi D, Duc NM, Xu J, Salas-Estrada L, Spasic A, Yun MW, Kang J, Gim D, Lee J, Du Y, Filizola M, Chung KY. Gαs slow conformational transition upon GTP binding and a novel Gαs regulator. iScience 2023; 26:106603. [PMID: 37128611 PMCID: PMC10148139 DOI: 10.1016/j.isci.2023.106603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023] Open
Abstract
G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR-G protein complex formation and guanosine diphosphate (GDP) release have been reported, no information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling framework that combines data from hydrogen-deuterium exchange mass spectrometry, tryptophan-induced fluorescence quenching, and metadynamics simulations to derive a kinetic model and atomic-level characterization of stepwise conformational changes incurred by the β2-adrenergic receptor (β2AR)-Gs complex after GDP release and GTP binding. Our data suggest rapid GTP binding and GTP-induced dissociation of Gαs from β2AR and Gβγ, as opposed to a slow closing of the Gαs α-helical domain (AHD). Yeast-two-hybrid screening using Gαs AHD as bait identified melanoma-associated antigen D2 (MAGE D2) as a novel AHD-binding protein, which was also shown to accelerate the GTP-induced closing of the Gαs AHD.
Collapse
Affiliation(s)
- Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Min Woo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Juyeong Kang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dongmin Gim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
116
|
Zhou Y, Ma X, Hu S, Yang S, Guo J, Li J, Zhang YF, Liu J, Qing Z, Yang R. Rigidity-Dependent Emission: Inspired Selection of an ATP-Specific Polyvalent Hydrogen Binding-Lighted Fluorophore for Intracellular Amplified Imaging. Anal Chem 2023; 95:8318-8324. [PMID: 37192373 DOI: 10.1021/acs.analchem.3c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
ATP, a small molecule with high intracellular concentration (mM level), provides a fuel to power signal amplification, which is meaningful for biosensing. However, traditional ATP-powered amplification is based on ATP/aptamer recognition, which is susceptible to the complex biological microenvironment (e.g., nuclease). In this work, we communicate a signaling manner termed as ATP-specific polyvalent hydrogen binding (APHB), which is mimetic to ATP/aptamer binding but can avoid interference from biomolecules. The key in APHB is a functional fluorophore that can selectively bind with ATP via polyvalent hydrogen, and the fluorescence was lighted with the changes of the molecular structure from flexibility to rigidity. By designing, synthesizing, and screening a series of compounds, we successfully obtained an ATP-specific binding-lighted fluorophore (ABF). Experimental verification and a complex analogue demonstrated that two melamine brackets in the ABF dominate the polyvalent hydrogen binding between the ABF and ATP. Then, to achieve amplification biosensing, fibroblast activation protein (FAP) in activated hepatic stellate cells was taken as a model target, and a nanobeacon consisting of an ABF, a quencher, and an FAP-activated polymer shell was constructed. Benefiting from the ATP-powered amplification, the FAP was sensitively detected and imaged, and the potential relationship between differentiation of hepatocytes and FAP concentration was first revealed, highlighting the great potential of APHB-mediated signaling for intracellular sensing.
Collapse
Affiliation(s)
- Yibo Zhou
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Xiaofei Ma
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Shan Hu
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Sheng Yang
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Jingru Guo
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Quality Control and Pharmacovigilance, Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Junbin Li
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Yue-Fei Zhang
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Ronghua Yang
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| |
Collapse
|
117
|
Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
Collapse
Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| |
Collapse
|
118
|
Gagelin A, Largeau C, Masscheleyn S, Piel MS, Calderón-Mora D, Bouillaud F, Hénin J, Miroux B. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling. Nat Commun 2023; 14:2594. [PMID: 37147287 PMCID: PMC10162991 DOI: 10.1038/s41467-023-38219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
Brown adipose tissue expresses uncoupling protein 1 (UCP1), which dissipates energy as heat, making it a target for treating metabolic disorders. Here, we investigate how purine nucleotides inhibit respiration uncoupling by UCP1. Our molecular simulations predict that GDP and GTP bind UCP1 in the common substrate binding site in an upright orientation, where the base moiety interacts with conserved residues R92 and E191. We identify a triplet of uncharged residues, F88/I187/W281, forming hydrophobic contacts with nucleotides. In yeast spheroplast respiration assays, both I187A and W281A mutants increase the fatty acid-induced uncoupling activity of UCP1 and partially suppress the inhibition of UCP1 activity by nucleotides. The F88A/I187A/W281A triple mutant is overactivated by fatty acids even at high concentrations of purine nucleotides. In simulations, E191 and W281 interact with purine but not pyrimidine bases. These results provide a molecular understanding of the selective inhibition of UCP1 by purine nucleotides.
Collapse
Affiliation(s)
- Antoine Gagelin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
| | - Corentin Largeau
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Sandrine Masscheleyn
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Mathilde S Piel
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Daniel Calderón-Mora
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Frédéric Bouillaud
- Université Paris Cité, Institut Cochin, Inserm U1016, CNRS UMR8104, Paris, 75014, France
| | - Jérôme Hénin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
| | - Bruno Miroux
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France.
| |
Collapse
|
119
|
Wong TS, Li G, Li S, Gao W, Chen G, Gan S, Zhang M, Li H, Wu S, Du Y. G protein-coupled receptors in neurodegenerative diseases and psychiatric disorders. Signal Transduct Target Ther 2023; 8:177. [PMID: 37137892 PMCID: PMC10154768 DOI: 10.1038/s41392-023-01427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 02/17/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Neuropsychiatric disorders are multifactorial disorders with diverse aetiological factors. Identifying treatment targets is challenging because the diseases are resulting from heterogeneous biological, genetic, and environmental factors. Nevertheless, the increasing understanding of G protein-coupled receptor (GPCR) opens a new possibility in drug discovery. Harnessing our knowledge of molecular mechanisms and structural information of GPCRs will be advantageous for developing effective drugs. This review provides an overview of the role of GPCRs in various neurodegenerative and psychiatric diseases. Besides, we highlight the emerging opportunities of novel GPCR targets and address recent progress in GPCR drug development.
Collapse
Affiliation(s)
- Thian-Sze Wong
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172, Shenzhen, Guangdong, China
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Guangzhi Li
- Institute of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, 518000, Shenzhen, Guangdong, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 200237, Shanghai, China
- Innovation Center for AI and Drug Discovery, East China Normal University, 200062, Shanghai, China
| | - Wei Gao
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172, Shenzhen, Guangdong, China
- Innovation Center for AI and Drug Discovery, East China Normal University, 200062, Shanghai, China
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172, Shenzhen, Guangdong, China
| | - Shiyi Gan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172, Shenzhen, Guangdong, China
| | - Manzhan Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 200237, Shanghai, China
- Innovation Center for AI and Drug Discovery, East China Normal University, 200062, Shanghai, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 200237, Shanghai, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, 200062, Shanghai, China.
| | - Song Wu
- Institute of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, 518000, Shenzhen, Guangdong, China.
- Department of Urology, South China Hospital, Health Science Center, Shenzhen University, 518116, Shenzhen, Guangdong, China.
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172, Shenzhen, Guangdong, China.
| |
Collapse
|
120
|
Chen JK, Merrick KA, Kong YW, Izrael-Tomasevic A, Eng G, Handly ED, Patterson JC, Cannell IG, Suarez-Lopez L, Hosios AM, Dinh A, Kirkpatrick DS, Yu K, Rose CM, Hernandez JM, Hwangbo H, Palmer AC, Vander Heiden MG, Yilmaz ÖH, Yaffe MB. An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538590. [PMID: 37162991 PMCID: PMC10168374 DOI: 10.1101/2023.04.28.538590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug's efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug's DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.
Collapse
Affiliation(s)
- Jung-Kuei Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karl A. Merrick
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - George Eng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erika D. Handly
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse C. Patterson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian G. Cannell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron M. Hosios
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anh Dinh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Kebing Yu
- Genentech Biotechnology company, South San Francisco, CA 94080, USA
| | | | - Jonathan M. Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haeun Hwangbo
- Curriculum in Bioinformatics and Computational Biology, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew G. Vander Heiden
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B. Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Surgery, Beth Israel Medical Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
121
|
Dupuy P, Glickman MS. The C-Terminal Acid Phosphatase Module of the RNase HI Enzyme RnhC Controls Rifampin Sensitivity and Light-Dependent Colony Pigmentation of Mycobacterium smegmatis. J Bacteriol 2023; 205:e0043122. [PMID: 36916909 PMCID: PMC10127661 DOI: 10.1128/jb.00431-22] [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: 11/12/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
RNase H enzymes participate in various processes that require processing of RNA-DNA hybrids, including DNA replication, transcription, and ribonucleotide excision from DNA. Mycobacteria encode multiple RNase H enzymes, and prior data indicate that RNase HI activity is essential for mycobacterial viability. However, the additional roles of mycobacterial RNase Hs are unknown, including whether RNase HII (RnhB and RnhD) excises chromosomal ribonucleotides misincorporated during DNA replication and whether individual RNase HI enzymes (RnhA and RnhC) mediate additional phenotypes. We find that loss of RNase HII activity in Mycobacterium smegmatis (through combined deletion of rnhB/rnhD) or individual RNase HI enzymes does not affect growth, hydroxyurea sensitivity, or mutagenesis, whereas overexpression (OE) of either RNase HII severely compromises bacterial viability. We also show that deletion of rnhC, which encodes a protein with an N-terminal RNase HI domain and a C-terminal acid phosphatase domain, confers sensitivity to rifampin and oxidative stress as well as loss of light-induced carotenoid pigmentation. These phenotypes are due to loss of the activity of the C-terminal acid phosphatase domain rather than the RNase HI activity, suggesting that the acid phosphatase activity may confer rifampin resistance through the antioxidant properties of carotenoid pigment production. IMPORTANCE Mycobacteria encode multiple RNase H enzymes, with RNase HI being essential for viability. Here, we examine additional functions of RNase H enzymes in mycobacteria. We find that RNase HII is not involved in mutagenesis but is highly toxic when overexpressed. The RNase HI enzyme RnhC is required for tolerance to rifampin, but this role is surprisingly independent of its RNase H activity and is instead mediated by an autonomous C-terminal acid phosphatase domain. This study provides new insights into the functions of the multiple RNase H enzymes of mycobacteria.
Collapse
Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, New York, New York, USA
| | - Michael S. Glickman
- Immunology Program, Sloan Kettering Institute, New York, New York, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, New York, USA
| |
Collapse
|
122
|
Sen D, Lazenby RA. Selective Aptamer Modification of Au Surfaces in a Microelectrode Sensor Array for Simultaneous Detection of Multiple Analytes. Anal Chem 2023; 95:6828-6835. [PMID: 37071798 DOI: 10.1021/acs.analchem.2c05335] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Aptamers have been employed as the biorecognition element in electrochemical aptamer-based (E-AB) biosensors, for the detection of a diverse range of analyte molecules, on electrodes with sizescales ranging from a few microns to several millimeters. Simultaneous detection of multiple different analytes requires the selective modification of multiple electrode surfaces with different aptamers. This process is typically achieved by incubating separate macroscale electrodes in a solution with the desired aptamer, which is unsuitable for microelectrode arrays in which the electrodes are closely spaced. In this work, we selectively modified electrode surfaces with thiolated aptamers of different single-stranded DNA sequences, by successive removal and addition of thiol monolayers. This was achieved by electrodesorption of thiol monolayers using controlled potential, to expose unmodified gold electrodes to be modified with a different thiolated aptamer, thus enabling multiple different aptamers to be used on the surfaces of closely spaced microelectrodes. All aptamers were methylene blue terminated, allowing redox currents to be measured and used to monitor aptamer probe packing density on the electrode surface and the selectivity of the sensors. Here, we demonstrate the microscale E-AB sensor multianalyte detection method using aptamers for target analytes, adenosine triphosphate, dopamine, and serotonin, which can ultimately be applied to perform localized simultaneous detection using electrode arrays.
Collapse
Affiliation(s)
- Debashis Sen
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
- Department of Chemistry, Faculty of Science, Comilla University, Cumilla 3506, Bangladesh
| | - Robert A Lazenby
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| |
Collapse
|
123
|
Mejia G, Su L, Pandey P, Jeanne Dit Fouque K, McGoron AJ, Fernandez-Lima F, He J, Mebel AM, Leng F. Anticancer Drug Doxorubicin Spontaneously Reacts with GTP and dGTP. Chem Res Toxicol 2023; 36:660-668. [PMID: 37000908 DOI: 10.1021/acs.chemrestox.2c00367] [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] [Indexed: 04/03/2023]
Abstract
Here, we reported a spontaneous reaction between anticancer drug doxorubicin and GTP or dGTP. Incubation of doxorubicin with GTP or dGTP at 37 °C or above yields a covalent product: the doxorubicin-GTP or -dGTP conjugate where a covalent bond is formed between the C14 position of doxorubicin and the 2-amino group of guanine. Density functional theory calculations show the feasibility of this spontaneous reaction. Fluorescence imaging studies demonstrate that the doxorubicin-GTP and -dGTP conjugates cannot enter nuclei although they rapidly accumulate in human SK-OV-3 and NCI/ADR-RES cells. Consequently, the doxorubicin-GTP and -dGTP conjugates are less cytotoxic than doxorubicin. We also demonstrate that doxorubicin binds to ATP, GTP, and other nucleotides with a dissociation constant (Kd) in the sub-millimolar range. Since human cells contain millimolar levels of ATP and GTP, these results suggest that doxorubicin may target ATP and GTP, energy molecules that support essential processes in living organisms.
Collapse
Affiliation(s)
- German Mejia
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Linjia Su
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Popular Pandey
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Kevin Jeanne Dit Fouque
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Anthony J McGoron
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Biomedical Engineering, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Jin He
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Alexander M Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
124
|
Martínez RAS, Pinky PD, Harlan BA, Brewer GJ. GTP energy dependence of endocytosis and autophagy in the aging brain and Alzheimer's disease. GeroScience 2023; 45:757-780. [PMID: 36622562 PMCID: PMC9886713 DOI: 10.1007/s11357-022-00717-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Increased interest in the aging and Alzheimer's disease (AD)-related impairments in autophagy in the brain raise important questions about regulation and treatment. Since many steps in endocytosis and autophagy depend on GTPases, new measures of cellular GTP levels are needed to evaluate energy regulation in aging and AD. The recent development of ratiometric GTP sensors (GEVALS) and findings that GTP levels are not homogenous inside cells raise new issues of regulation of GTPases by the local availability of GTP. In this review, we highlight the metabolism of GTP in relation to the Rab GTPases involved in formation of early endosomes, late endosomes, and lysosomal transport to execute the autophagic degradation of damaged cargo. Specific GTPases control macroautophagy (mitophagy), microautophagy, and chaperone-mediated autophagy (CMA). By inference, local GTP levels would control autophagy, if not in excess. Additional levels of control are imposed by the redox state of the cell, including thioredoxin involvement. Throughout this review, we emphasize the age-related changes that could contribute to deficits in GTP and AD. We conclude with prospects for boosting GTP levels and reversing age-related oxidative redox shift to restore autophagy. Therefore, GTP levels could regulate the numerous GTPases involved in endocytosis, autophagy, and vesicular trafficking. In aging, metabolic adaptation to a sedentary lifestyle could impair mitochondrial function generating less GTP and redox energy for healthy management of amyloid and tau proteostasis, synaptic function, and inflammation.
Collapse
Affiliation(s)
| | - Priyanka D. Pinky
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Benjamin A. Harlan
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Gregory J. Brewer
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
- Center for Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA 92697 USA
- MIND Institute, University of California Irvine, Irvine, CA 92697 USA
| |
Collapse
|
125
|
Mannherz W, Agarwal S. Thymidine nucleotide metabolism controls human telomere length. Nat Genet 2023; 55:568-580. [PMID: 36959362 PMCID: PMC11000509 DOI: 10.1038/s41588-023-01339-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
Abstract
Telomere length in humans is associated with lifespan and severe diseases, yet the genetic determinants of telomere length remain incompletely defined. Here we performed genome-wide CRISPR-Cas9 functional telomere length screening and identified thymidine (dT) nucleotide metabolism as a limiting factor in human telomere maintenance. Targeted genetic disruption using CRISPR-Cas9 revealed multiple telomere length control points across the thymidine nucleotide metabolism pathway: decreasing dT nucleotide salvage via deletion of the gene encoding nuclear thymidine kinase (TK1) or de novo production by knockout of the thymidylate synthase gene (TYMS) decreased telomere length, whereas inactivation of the deoxynucleoside triphosphohydrolase-encoding gene SAMHD1 lengthened telomeres. Remarkably, supplementation with dT alone drove robust telomere elongation by telomerase in cells, and thymidine triphosphate stimulated telomerase activity in a substrate-independent manner in vitro. In induced pluripotent stem cells derived from patients with genetic telomere biology disorders, dT supplementation or inhibition of SAMHD1 promoted telomere restoration. Our results demonstrate a critical role of thymidine metabolism in controlling human telomerase and telomere length, which may be therapeutically actionable in patients with fatal degenerative diseases.
Collapse
Affiliation(s)
- William Mannherz
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard/MIT MD-PhD Program, Harvard Stem Cell Institute, Harvard Initiative for RNA Medicine, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Biological and Biomedical Sciences Program, Harvard/MIT MD-PhD Program, Harvard Stem Cell Institute, Harvard Initiative for RNA Medicine, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
126
|
Doke AA, Jha SK. Shapeshifter TDP-43: Molecular mechanism of structural polymorphism, aggregation, phase separation and their modulators. Biophys Chem 2023; 295:106972. [PMID: 36812677 DOI: 10.1016/j.bpc.2023.106972] [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: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
TDP-43 is a nucleic acid-binding protein that performs physiologically essential functions and is known to undergo phase separation and aggregation during stress. Initial observations have shown that TDP-43 forms heterogeneous assemblies, including monomer, dimer, oligomers, aggregates, phase-separated assemblies, etc. However, the significance of each assembly of TDP-43 concerning its function, phase separation, and aggregation is poorly known. Furthermore, how different assemblies of TDP-43 are related to each other is unclear. In this review, we focus on the various assemblies of TDP-43 and discuss the plausible origin of the structural heterogeneity of TDP-43. TDP-43 is involved in multiple physiological processes like phase separation, aggregation, prion-like seeding, and performing physiological functions. However, the molecular mechanism behind the physiological process performed by TDP-43 is not well understood. The current review discusses the plausible molecular mechanism of phase separation, aggregation, and prion-like propagation of TDP-43.
Collapse
Affiliation(s)
- Abhilasha A Doke
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
127
|
Zacharchenko T, Dorendorf T, Locker N, Van Dijk E, Katzemich A, Diederichs K, Bullard B, Mayans O. PK1 from Drosophila obscurin is an inactive pseudokinase with scaffolding properties. Open Biol 2023; 13:220350. [PMID: 37121260 PMCID: PMC10129394 DOI: 10.1098/rsob.220350] [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: 11/25/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Obscurins are large filamentous proteins with crucial roles in the assembly, stability and regulation of muscle. Characteristic of these proteins is a tandem of two C-terminal kinase domains, PK1 and PK2, that are separated by a long intrinsically disordered sequence. The significance of this conserved domain arrangement is unknown. Our study of PK1 from Drosophila obscurin shows that this is a pseudokinase with features typical of the CAM-kinase family, but which carries a minimalistic regulatory tail that no longer binds calmodulin or has mechanosensory properties typical of other sarcomeric kinases. PK1 binds ATP with high affinity, but in the absence of magnesium and lacks detectable phosphotransfer activity. It also has a highly diverged active site, strictly conserved across arthropods, that might have evolved to accommodate an unconventional binder. We find that PK1 interacts with PK2, suggesting a functional relation to the latter. These findings lead us to speculate that PK1/PK2 form a pseudokinase/kinase dual system, where PK1 might act as an allosteric regulator of PK2 and where mechanosensing properties, akin to those described for regulatory tails in titin-like kinases, might now reside on the unstructured interkinase segment. We propose that the PK1-interkinase-PK2 region constitutes an integrated functional unit in obscurin proteins.
Collapse
Affiliation(s)
- Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Till Dorendorf
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Evert Van Dijk
- Biosynth B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
| | | | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
128
|
Bré J, Dickson AL, Read OJ, Zhang Y, McKissock FG, Mullen P, Tang P, Zickuhr GM, Czekster CM, Harrison DJ. The novel anti-cancer fluoropyrimidine NUC-3373 is a potent inhibitor of thymidylate synthase and an effective DNA-damaging agent. Cancer Chemother Pharmacol 2023; 91:401-412. [PMID: 37000221 PMCID: PMC10156769 DOI: 10.1007/s00280-023-04528-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
INTRODUCTION Fluoropyrimidines, principally 5-fluorouracil (5-FU), remain a key component of chemotherapy regimens for multiple cancer types, in particular colorectal and other gastrointestinal malignancies. To overcome key limitations and pharmacologic challenges that hinder the clinical utility of 5-FU, NUC-3373, a phosphoramidate transformation of 5-fluorodeoxyuridine, was designed to improve the efficacy and safety profile as well as the administration challenges associated with 5-FU. METHODS Human colorectal cancer cell lines HCT116 and SW480 were treated with sub-IC50 doses of NUC-3373 or 5-FU. Intracellular activation was measured by LC-MS. Western blot was performed to determine binding of the active anti-cancer metabolite FdUMP to thymidylate synthase (TS) and DNA damage. RESULTS We demonstrated that NUC-3373 generates more FdUMP than 5-FU, resulting in a more potent inhibition of TS, DNA misincorporation and subsequent cell cycle arrest and DNA damage in vitro. Unlike 5-FU, the thymineless death induced by NUC-3373 was rescued by the concurrent addition of exogenous thymidine. 5-FU cytotoxicity, however, was only reversed by supplementation with uridine, a treatment used to reduce 5-FU-induced toxicities in the clinic. This is in line with our findings that 5-FU generates FUTP which is incorporated into RNA, a mechanism known to underlie the myelosuppression and gastrointestinal inflammation associated with 5-FU. CONCLUSION Taken together, these results highlight key differences between NUC-3373 and 5-FU that are driven by the anti-cancer metabolites generated. NUC-3373 is a potent inhibitor of TS that also causes DNA-directed damage. These data support the preliminary clinical evidence that suggest NUC-3373 has a favorable safety profile in patients.
Collapse
Affiliation(s)
- Jennifer Bré
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
- NuCana Plc, 3 Lochside Way, Edinburgh, EH12 9DT, UK.
| | - Alison L Dickson
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
- NuCana Plc, 3 Lochside Way, Edinburgh, EH12 9DT, UK
| | - Oliver J Read
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
- NuCana Plc, 3 Lochside Way, Edinburgh, EH12 9DT, UK
| | - Ying Zhang
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | | | - Peter Mullen
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Peijun Tang
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Greice M Zickuhr
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Clarissa M Czekster
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - David J Harrison
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
- NuCana Plc, 3 Lochside Way, Edinburgh, EH12 9DT, UK
| |
Collapse
|
129
|
Huang SK, Picard LP, Rahmatullah RSM, Pandey A, Van Eps N, Sunahara RK, Ernst OP, Sljoka A, Prosser RS. Mapping the conformational landscape of the stimulatory heterotrimeric G protein. Nat Struct Mol Biol 2023; 30:502-511. [PMID: 36997760 DOI: 10.1038/s41594-023-00957-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
Heterotrimeric G proteins serve as membrane-associated signaling hubs, in concert with their cognate G-protein-coupled receptors. Fluorine nuclear magnetic resonance spectroscopy was employed to monitor the conformational equilibria of the human stimulatory G-protein α subunit (Gsα) alone, in the intact Gsαβ1γ2 heterotrimer or in complex with membrane-embedded human adenosine A2A receptor (A2AR). The results reveal a concerted equilibrium that is strongly affected by nucleotide and interactions with the βγ subunit, the lipid bilayer and A2AR. The α1 helix of Gsα exhibits significant intermediate timescale dynamics. The α4β6 loop and α5 helix undergo membrane/receptor interactions and order-disorder transitions respectively, associated with G-protein activation. The αN helix adopts a key functional state that serves as an allosteric conduit between the βγ subunit and receptor, while a significant fraction of the ensemble remains tethered to the membrane and receptor upon activation.
Collapse
Affiliation(s)
- Shuya Kate Huang
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | | | - Rima S M Rahmatullah
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | - Aditya Pandey
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan.
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
130
|
Wang C, Yu L, Zhang J, Zhou Y, Sun B, Xiao Q, Zhang M, Liu H, Li J, Li J, Luo Y, Xu J, Lian Z, Lin J, Wang X, Zhang P, Guo L, Ren R, Deng D. Structural basis of the substrate recognition and inhibition mechanism of Plasmodium falciparum nucleoside transporter PfENT1. Nat Commun 2023; 14:1727. [PMID: 36977719 PMCID: PMC10050424 DOI: 10.1038/s41467-023-37411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
By lacking de novo purine biosynthesis enzymes, Plasmodium falciparum requires purine nucleoside uptake from host cells. The indispensable nucleoside transporter ENT1 of P. falciparum facilitates nucleoside uptake in the asexual blood stage. Specific inhibitors of PfENT1 prevent the proliferation of P. falciparum at submicromolar concentrations. However, the substrate recognition and inhibitory mechanism of PfENT1 are still elusive. Here, we report cryo-EM structures of PfENT1 in apo, inosine-bound, and inhibitor-bound states. Together with in vitro binding and uptake assays, we identify that inosine is the primary substrate of PfENT1 and that the inosine-binding site is located in the central cavity of PfENT1. The endofacial inhibitor GSK4 occupies the orthosteric site of PfENT1 and explores the allosteric site to block the conformational change of PfENT1. Furthermore, we propose a general "rocker switch" alternating access cycle for ENT transporters. Understanding the substrate recognition and inhibitory mechanisms of PfENT1 will greatly facilitate future efforts in the rational design of antimalarial drugs.
Collapse
Affiliation(s)
- Chen Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Leiye Yu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
- Warshal Institute of Computational Biology, School of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Jiying Zhang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Yanxia Zhou
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Qingjie Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Minhua Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huayi Liu
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinhong Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Jialu Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of MOE, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jie Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhong Lian
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingwen Lin
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiang Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Li Guo
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
- Shanghai Qi Zhi Institute, Shanghai, 200030, China.
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, 610041, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
131
|
Abstract
Metabolic alterations are a key hallmark of cancer cells, and the augmented synthesis and use of nucleotide triphosphates is a critical and universal metabolic dependency of cancer cells across different cancer types and genetic backgrounds. Many of the aggressive behaviours of cancer cells, including uncontrolled proliferation, chemotherapy resistance, immune evasion and metastasis, rely heavily on augmented nucleotide metabolism. Furthermore, most of the known oncogenic drivers upregulate nucleotide biosynthetic capacity, suggesting that this phenotype is a prerequisite for cancer initiation and progression. Despite the wealth of data demonstrating the efficacy of nucleotide synthesis inhibitors in preclinical cancer models and the well-established clinical use of these drugs in certain cancer settings, the full potential of these agents remains unrealized. In this Review, we discuss recent studies that have generated mechanistic insights into the diverse biological roles of hyperactive cancer cell nucleotide metabolism. We explore opportunities for combination therapies that are highlighted by these recent advances and detail key questions that remain to be answered, with the goal of informing urgently warranted future studies.
Collapse
Affiliation(s)
- Nicholas J Mullen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pankaj K Singh
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| |
Collapse
|
132
|
Sheng C, Zhao J, Yu F, Li L. Enzyme Translocation-Mediated Signal Amplification for Spatially Selective Aptasensing of ATP in Inflammatory Cells. Angew Chem Int Ed Engl 2023; 62:e202217551. [PMID: 36750407 DOI: 10.1002/anie.202217551] [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: 11/29/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 02/09/2023]
Abstract
Amplified ATP imaging in inflammatory cells is highly desirable. However, the spatial selectivity of current amplification methods is limited, that is, signal amplification is performed systemically and not in a disease site-specific manner. Here we present a versatile strategy, termed enzymatically triggerable, aptamer-based signal amplification (ETA-SA), that enables inflammatory cell-specific imaging of ATP through spatially-resolved signal amplification. The ETA-SA leverages a translocated enzyme in inflammatory cells to activate DNA aptamer probes and further drive cascade reactions through the consumption of hairpin fuels, which, however, exerts no ATP response activity in normal cells, leading to a significantly improved sensitivity and spatial specificity for the inflammation-specific ATP imaging in vivo. Benefiting from the improved spatial selectivity, enhanced signal-to-background ratios were achieved for ATP imaging during acute hepatitis.
Collapse
Affiliation(s)
- Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
133
|
Arı M, Sağdilek E, Kılınç E, Cansev M, Özlük K. Effects of uridine and nucleotides on hemostasis parameters. J Thromb Thrombolysis 2023; 55:626-633. [PMID: 36961669 DOI: 10.1007/s11239-023-02793-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/08/2023] [Indexed: 03/25/2023]
Abstract
Several purinergic receptors have been identified on platelets which are involved in hemostatic and thrombotic processes. The aim of the present study was to investigate the effects of uridine and its nucleotides on platelet aggregation and hemostasis in platelet-rich plasma (PRP) and whole blood. The effects of uridine, UMP, UDP, and UTP at different final concentrations (1 to 1000 µM) on platelet aggregation were studied using an aggregometer. In PRP samples, platelet aggregation was induced by ADP, collagen and epinephrine 3 min after addition of uridine, UMP, UDP, UTP and saline (as a control). All thromboelastogram experiments were performed at 1000 µM final concentrations of uridine and its nucleotides in whole blood. UDP and UTP were also tested in thromboelastogram with PRP. Our results showed that UDP, and especially UTP, inhibited ADP- and collagen-induced aggregation in a concentration-dependent manner. In whole blood thromboelastogram experiments, UDP stimulated clot formation while UTP suppressed clot formation. When thromboelastogram experiments were repeated with PRP, UTP's inhibitory effect on platelets was confirmed, while UDP's stimulated clot forming effect disappeared. Collectively, our data showed that UTP inhibited platelet aggregation in a concentration-dependent manner and suppressed clot formation. On the other hand, UDP exhibited distinct effects on whole blood or PRP in thromboelastogram. These data suggest that the difference on effects of UTP and UDP might have arisen from the different receptors that they stimulate and warrant further investigation with regard to their in vivo actions on platelet aggregation and hemostasis.
Collapse
Affiliation(s)
- Merve Arı
- Vocational School of Health Services, KTO Karatay University, Konya, Turkey
| | - Engin Sağdilek
- School of Medicine, Department of Biophysics, Bursa Uludağ University, Bursa, 16059, Turkey.
| | - Evren Kılınç
- School of Medicine, Department of Biophysics, Acıbadem University, İstanbul, Turkey
| | - Mehmet Cansev
- School of Medicine, Department of Pharmacology, Bursa Uludağ University, Bursa, Turkey
| | - Kasım Özlük
- School of Medicine, Department of Physiology, Bursa Uludağ University, Bursa, Turkey
| |
Collapse
|
134
|
Borges JI, Suster MS, Lymperopoulos A. Cardiac RGS Proteins in Human Heart Failure and Atrial Fibrillation: Focus on RGS4. Int J Mol Sci 2023; 24:ijms24076136. [PMID: 37047106 PMCID: PMC10147095 DOI: 10.3390/ijms24076136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
The regulator of G protein signaling (RGS) proteins are crucial for the termination of G protein signals elicited by G protein-coupled receptors (GPCRs). This superfamily of cell membrane receptors, by far the largest and most versatile in mammals, including humans, play pivotal roles in the regulation of cardiac function and homeostasis. Perturbations in both the activation and termination of their G protein-mediated signaling underlie numerous heart pathologies, including heart failure (HF) and atrial fibrillation (AFib). Therefore, RGS proteins play important roles in the pathophysiology of these two devasting cardiac diseases, and several of them could be targeted therapeutically. Although close to 40 human RGS proteins have been identified, each RGS protein seems to interact only with a specific set of G protein subunits and GPCR types/subtypes in any given tissue or cell type. Numerous in vitro and in vivo studies in animal models, and also in diseased human heart tissue obtained from transplantations or tissue banks, have provided substantial evidence of the roles various cardiomyocyte RGS proteins play in cardiac normal homeostasis as well as pathophysiology. One RGS protein in particular, RGS4, has been reported in what are now decades-old studies to be selectively upregulated in human HF. It has also been implicated in protection against AFib via knockout mice studies. This review summarizes the current understanding of the functional roles of cardiac RGS proteins and their implications for the treatment of HF and AFib, with a specific focus on RGS4 for the aforementioned reasons but also because it can be targeted successfully with small organic molecule inhibitors.
Collapse
Affiliation(s)
- Jordana I Borges
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
| | - Malka S Suster
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
| | - Anastasios Lymperopoulos
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
| |
Collapse
|
135
|
Papasergi-Scott MM, Pérez-Hernández G, Batebi H, Gao Y, Eskici G, Seven AB, Panova O, Hilger D, Casiraghi M, He F, Maul L, Gmeiner P, Kobilka BK, Hildebrand PW, Skiniotis G. Time-resolved cryo-EM of G protein activation by a GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533387. [PMID: 36993214 PMCID: PMC10055275 DOI: 10.1101/2023.03.20.533387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
G protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating the exchange of guanine nucleotide in the Gα subunit. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G protein complex. Using variability analysis to monitor the transitions of the stimulatory Gs protein in complex with the β 2 -adrenergic receptor (β 2 AR) at short sequential time points after GTP addition, we identified the conformational trajectory underlying G protein activation and functional dissociation from the receptor. Twenty transition structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of events driving G protein activation upon GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα Switch regions and the α5 helix that weaken the G protein-receptor interface. Molecular dynamics (MD) simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP upon closure of the alpha-helical domain (AHD) against the nucleotide-bound Ras-homology domain (RHD) correlates with irreversible α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signaling events.
Collapse
|
136
|
Liu M, Chen H, Huang Y, Liu J, Chen Q, Zuo H, Fang L, Mao C. Enriching adenosine by thymine-rich DNA oligomers. Analyst 2023; 148:1858-1866. [PMID: 36942467 DOI: 10.1039/d3an00297g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Adenosine levels are important in various physiological and pathological activities, but detecting them is difficult because of interference from a complex matrix. This study designed a series of DNA oligomers rich in thymine to enrich adenosine. Their binding affinity (Kd range: 1.25-5.0 mM) to adenosine varied based on the DNA secondary structures, with a clamped hairpin structure showing the highest binding affinity. Compared to other designs, this clamped DNA hairpin underwent the least conformational change during adenosine binding. These DNAs also suppressed the precipitation of supersaturated adenine. Taken together, these results suggest that thymine-rich DNAs could be used to enrich and separate adenosine.
Collapse
Affiliation(s)
- Mingchun Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Huaiqing Chen
- Biological Sciences Research Center, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Yuhan Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jian Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Qianfeng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Liang Fang
- Department of Oncology, The Ninth Chongqing People's Hospital, Chongqing 400700, China.
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette 47907, IN, USA.
| |
Collapse
|
137
|
Hicks KG, Cluntun AA, Schubert HL, Hackett SR, Berg JA, Leonard PG, Ajalla Aleixo MA, Zhou Y, Bott AJ, Salvatore SR, Chang F, Blevins A, Barta P, Tilley S, Leifer A, Guzman A, Arok A, Fogarty S, Winter JM, Ahn HC, Allen KN, Block S, Cardoso IA, Ding J, Dreveny I, Gasper WC, Ho Q, Matsuura A, Palladino MJ, Prajapati S, Sun P, Tittmann K, Tolan DR, Unterlass J, VanDemark AP, Vander Heiden MG, Webb BA, Yun CH, Zhao P, Wang B, Schopfer FJ, Hill CP, Nonato MC, Muller FL, Cox JE, Rutter J. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science 2023; 379:996-1003. [PMID: 36893255 PMCID: PMC10262665 DOI: 10.1126/science.abm3452] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
Collapse
Affiliation(s)
- Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Jordan A Berg
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariana A Ajalla Aleixo
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Alex J Bott
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aubrie Blevins
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paige Barta
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Samantha Tilley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron Leifer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea Guzman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ajak Arok
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hee-Chul Ahn
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Samuel Block
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Quinn Ho
- Department of Biology, Boston University, Boston, MA, USA
| | - Atsushi Matsuura
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, MA, USA
| | - Judith Unterlass
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV, USA
| | - Cai-Hong Yun
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengkai Zhao
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
- Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
138
|
In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity. Int J Mol Sci 2023; 24:ijms24065120. [PMID: 36982188 PMCID: PMC10049026 DOI: 10.3390/ijms24065120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).
Collapse
|
139
|
Yin X, Wang W, Seah SYK, Mine Y, Fan MZ. Deglycosylation Differentially Regulates Weaned Porcine Gut Alkaline Phosphatase Isoform Functionality along the Longitudinal Axis. Pathogens 2023; 12:pathogens12030407. [PMID: 36986329 PMCID: PMC10053101 DOI: 10.3390/pathogens12030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Gut alkaline phosphatases (AP) dephosphorylate the lipid moiety of endotoxin and other pathogen-associated-molecular patterns members, thus maintaining gut eubiosis and preventing metabolic endotoxemia. Early weaned pigs experience gut dysbiosis, enteric diseases and growth retardation in association with decreased intestinal AP functionality. However, the role of glycosylation in modulation of the weaned porcine gut AP functionality is unclear. Herein three different research approaches were taken to investigate how deglycosylation affected weaned porcine gut AP activity kinetics. In the first approach, weaned porcine jejunal AP isoform (IAP) was fractionated by the fast protein-liquid chromatography and purified IAP fractions were kinetically characterized to be the higher-affinity and lower-capacity glycosylated mature IAP (p < 0.05) in comparison with the lower-affinity and higher-capacity non-glycosylated pre-mature IAP. The second approach enzyme activity kinetic analyses showed that N-deglycosylation of AP by the peptide N-glycosidase-F enzyme reduced (p < 0.05) the IAP maximal activity in the jejunum and ileum and decreased AP affinity (p < 0.05) in the large intestine. In the third approach, the porcine IAP isoform-X1 (IAPX1) gene was overexpressed in the prokaryotic ClearColiBL21 (DE3) cell and the recombinant porcine IAPX1 was associated with reduced (p < 0.05) enzyme affinity and maximal enzyme activity. Therefore, levels of glycosylation can modulate plasticity of weaned porcine gut AP functionality towards maintaining gut microbiome and the whole-body physiological status.
Collapse
Affiliation(s)
- Xindi Yin
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Canadian Food Inspection Agency (CFIA)-Ontario Operation, Guelph, ON N1G 4S9, Canada
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Ming Z. Fan
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- One Health Institute, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
| |
Collapse
|
140
|
Tew DJ, Hebert JM, Schmier BJ. Discovery and properties of a monoclonal antibody targeting 8-oxoA, an oxidized adenine lesion in DNA and RNA. Redox Biol 2023; 62:102658. [PMID: 36989571 PMCID: PMC10074937 DOI: 10.1016/j.redox.2023.102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/17/2023] Open
Abstract
8-oxoA, a major oxidation product of adenosine, is a mispairing, mutagenic lesion that arises in DNA and RNA when •OH radicals or one-electron oxidants attack the C8 adenine atom or polymerases misincorporate 8-oxo(d)ATP. The danger of 8-oxoA is underscored by the existence of dedicated cellular repair machinery that explicitly excise it from DNA, the attenuation of translation induced by 8-oxoA-mRNA or damaged ribosomes, and its potency as a TLR7 agonist. Here we present the discovery, purification, and biochemical characterization of a new mouse IgGk1 monoclonal antibody (6E4) that specifically targets 8-oxoA. Utilizing an AchE-based competitive ELISA assay, we demonstrate the selectivity of 6E4 for 8-oxoA over a plethora of canonical and chemically modified nucleosides including 8-oxoG, A, m6A, 2-oxoA, and 5-hoU. We further show the ability of 6E4 to exclusively recognize 8-oxoA in nucleoside triphosphates (8-oxoATP) and DNA/RNA oligonucleotides containing a single 8-oxoA. 6E4 also binds 8-oxoA in duplex DNA/RNA antigens where the lesion is either paired correctly or base mismatched. Our findings define the 8-oxoAde nucleobase as the critical epitope and indicate mAb 6E4 is ideally suited for a broad range of immunological applications in nucleic acid detection and quality control.
Collapse
|
141
|
Li J, Zhang H, Wang ZH, Li YX, Zhang LQ, Cui J, Li DN, Wang ZH, Liu Q, Liu Z, Iwakuma T, Cai JP. 8-oxo-dGTP curbs tumor development via S phase arrest and AIF-mediated apoptosis. Free Radic Biol Med 2023; 196:53-64. [PMID: 36640852 DOI: 10.1016/j.freeradbiomed.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Oxidative stress can attack precursor nucleotides, resulting in nucleic acid damage in cells. It remains unclear how 8-oxo-dGTP and 8-oxoGTP, oxidized forms of dGTP and GTP, respectively, could affect DNA or RNA oxidation levels and tumor development. To address this, we intravenously administered 8-oxo-dGTP and 8-oxoGTP to wild-type and MTH1-knockout mice. 8-oxoGTP administration increased frequency of tumor incidence, which is more prominent in MTH1-knockout mice. However, 8-oxo-dGTP treatment rather reduced tumor development regardless of the mouse genotype. The tumor suppressive effects of 8-oxo-dGTP were further confirmed using xenograft and C57/6J-ApcMin/Nju mouse models. Mechanistically, 8-oxo-dGTP increased the 8-oxo-dG contents in DNA and DNA strand breakage, induced cell cycle arrest in S phase and apoptosis mediated by AIF, eventually leading to reduced tumor incidence. These results suggest distinct roles of 8-oxo-dGTP and 8-oxoGTP in tumor development.
Collapse
Affiliation(s)
- Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - He Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, PR China
| | - Zhen-He Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Yun-Xuan Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Ju Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Dan-Ni Li
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Qian Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zhen Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Tomoo Iwakuma
- Children's Mercy Research Institute, Kansas City, MO, 64108, USA
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| |
Collapse
|
142
|
Structural and Functional Implication of Natural Variants of Gαs. Int J Mol Sci 2023; 24:ijms24044064. [PMID: 36835474 PMCID: PMC9959179 DOI: 10.3390/ijms24044064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are among the most important cellular signaling components, especially G protein-coupled receptors (GPCRs). G proteins comprise three subunits, Gα, Gβ, and Gγ. Gα is the key subunit, and its structural state regulates the active status of G proteins. Interaction of guanosine diphosphate (GDP) or guanosine triphosphate (GTP) with Gα switches G protein into basal or active states, respectively. Genetic alteration in Gα could be responsible for the development of various diseases due to its critical role in cell signaling. Specifically, loss-of-function mutations of Gαs are associated with parathyroid hormone-resistant syndrome such as inactivating parathyroid hormone/parathyroid hormone-related peptide (PTH/PTHrP) signaling disorders (iPPSDs), whereas gain-of-function mutations of Gαs are associated with McCune-Albright syndrome and tumor development. In the present study, we analyzed the structural and functional implications of natural variants of the Gαs subtype observed in iPPSDs. Although a few tested natural variants did not alter the structure and function of Gαs, others induced drastic conformational changes in Gαs, resulting in improper folding and aggregation of the proteins. Other natural variants induced only mild conformational changes but altered the GDP/GTP exchange kinetics. Therefore, the results shed light on the relationship between natural variants of Gα and iPPSDs.
Collapse
|
143
|
Tamima U, Sarkar S, Islam MR, Shil A, Kim KH, Reo YJ, Jun YW, Banna H, Lee S, Ahn KH. A Small-Molecule Fluorescence Probe for Nuclear ATP. Angew Chem Int Ed Engl 2023; 62:e202300580. [PMID: 36792537 DOI: 10.1002/anie.202300580] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/17/2023]
Abstract
Fluorescence monitoring of ATP in different organelles is now feasible with a few biosensors developed, which, however, show low sensitivity, limited biocompatibility, and accessibility. Small-molecule ATP probes that alleviate those limitations thus have received much attention recently, leading to a few ATP probes that target several organelles except for the nucleus. We disclose the first small-molecule probe that selectively detects nuclear ATP through reversible binding, with 25-fold fluorescence enhancement at pH 7.4 and excellent selectivity against various biologically relevant species. Using the probe, we observed 2.1-3.3-fold and 3.9-7.8-fold higher nuclear ATP levels in cancerous cell lines and tumor tissues compared with normal cell lines and tissues, respectively, which are explained by the higher nuclear ATP level in the mitosis phase. The probe has great potential for studying nuclear ATP-associated biology.
Collapse
Affiliation(s)
- Umme Tamima
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Sourav Sarkar
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Md Reyazul Islam
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Anushree Shil
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Kyeong Hwan Kim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Ye Jin Reo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Yong Woong Jun
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Hasanul Banna
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Soobin Lee
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| | - Kyo Han Ahn
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673 (Republic of, Korea
| |
Collapse
|
144
|
Hewitt N, Ma N, Arang N, Martin SA, Prakash A, DiBerto JF, Knight KM, Ghosh S, Olsen RHJ, Roth BL, Gutkind JS, Vaidehi N, Campbell SL, Dohlman HG. Catalytic site mutations confer multiple states of G protein activation. Sci Signal 2023; 16:eabq7842. [PMID: 36787384 PMCID: PMC10021883 DOI: 10.1126/scisignal.abq7842] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) that function as molecular switches for cellular growth and metabolism are activated by GTP and inactivated by GTP hydrolysis. In uveal melanoma, a conserved glutamine residue critical for GTP hydrolysis in the G protein α subunit is often mutated in Gαq or Gα11 to either leucine or proline. In contrast, other glutamine mutations or mutations in other Gα subtypes are rare. To uncover the mechanism of the genetic selection and the functional role of this glutamine residue, we analyzed all possible substitutions of this residue in multiple Gα isoforms. Through cell-based measurements of activity, we showed that some mutants were further activated and inactivated by G protein-coupled receptors. Through biochemical, molecular dynamics, and nuclear magnetic resonance-based structural studies, we showed that the Gα mutants were functionally distinct and conformationally diverse, despite their shared inability to hydrolyze GTP. Thus, the catalytic glutamine residue contributes to functions beyond GTP hydrolysis, and these functions include subtype-specific, allosteric modulation of receptor-mediated subunit dissociation. We conclude that G proteins do not function as simple on-off switches. Rather, signaling emerges from an ensemble of active states, a subset of which are favored in disease and may be uniquely responsive to receptor-directed ligands.
Collapse
Affiliation(s)
- Natalie Hewitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Nadia Arang
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Sarah A. Martin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey F. DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Soumadwip Ghosh
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Current address: Illumina Inc, 5200 Illumina Way, San Diego, CA 92037, USA
| | - Reid H. J. Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Current address: GPCR Pharmacology, Discovery Biology, Exscientia Ai, Oxford, UK OX4 4GE
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Silvio Gutkind
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
145
|
Yang W, Mixich L, Boonstra E, Cabral H. Polymer-Based mRNA Delivery Strategies for Advanced Therapies. Adv Healthc Mater 2023:e2202688. [PMID: 36785927 DOI: 10.1002/adhm.202202688] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Messenger RNA (mRNA)-based therapies offer great promise for the treatment of a variety of diseases. In 2020, two FDA approvals of mRNA-based vaccines have elevated mRNA vaccines to global recognition. However, the therapeutic capabilities of mRNA extend far beyond vaccines against infectious diseases. They hold potential for cancer vaccines, protein replacement therapies, gene editing therapies, and immunotherapies. For realizing such advanced therapies, it is crucial to develop effective carrier systems. Recent advances in materials science have led to the development of promising nonviral mRNA delivery systems. In comparison to other carriers like lipid nanoparticles, polymer-based delivery systems often receive less attention, despite their unique ability to carefully tune their chemical features to promote mRNA protection, their favorable pharmacokinetics, and their potential for targeting delivery. In this review, the central features of polymer-based systems for mRNA delivery highlighting the molecular design criteria, stability, and biodistribution are discussed. Finally, the role of targeting ligands for the future of RNA therapies is analyzed.
Collapse
Affiliation(s)
- Wenqian Yang
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Lucas Mixich
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Eger Boonstra
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| |
Collapse
|
146
|
Rodríguez LC, Foressi NN, Celej MS. Modulation of α-synuclein phase separation by biomolecules. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140885. [PMID: 36481455 DOI: 10.1016/j.bbapap.2022.140885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Liquid-liquid phase separation (LLPS) is currently recognized as a common mechanism involved in the regulation of a number of cellular functions. On the other hand, aberrant phase separation has been linked to the biogenesis of several neurodegenerative disorders since many proteins that undergo LLPS are also found in pathological aggregates. The formation of mixed protein coacervates may constitute a risk factor in overlapping neuropathologies, such as Parkinson's (PD) and Alzheimer's (AD) diseases. In this work, we evaluated the homotypic and heterotypic phase behaviour of the PD-related protein α-synuclein (AS) in the presence of the biologically relevant molecules ATP, polyamines, and the AD-related protein Tau. We found that AS exhibits a low propensity to form homotypic liquid droplets, yet phase separates into liquid-like or solid-like phases depending on the interacting biomolecule. We further demonstrated the synergistic droplet formation of AS and Tau providing support for a mechanism in which mixed condensates might contribute to the biogenesis of AS/Tau pathologies.
Collapse
Affiliation(s)
- Leandro Cruz Rodríguez
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Nahuel N Foressi
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
| |
Collapse
|
147
|
Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
Collapse
Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
| |
Collapse
|
148
|
Shin J, Mir H, Khurram MA, Fujihara KM, Dynlacht BD, Cardozo TJ, Possemato R. Allosteric regulation of CAD modulates de novo pyrimidine synthesis during the cell cycle. Nat Metab 2023; 5:277-293. [PMID: 36747088 PMCID: PMC10064490 DOI: 10.1038/s42255-023-00735-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/03/2023] [Indexed: 02/08/2023]
Abstract
Metabolism is a fundamental cellular process that is coordinated with cell cycle progression. Despite this association, a mechanistic understanding of cell cycle phase-dependent metabolic pathway regulation remains elusive. Here we report the mechanism by which human de novo pyrimidine biosynthesis is allosterically regulated during the cell cycle. Combining traditional synchronization methods and metabolomics, we characterize metabolites by their accumulation pattern during cell cycle phases and identify cell cycle phase-dependent regulation of carbamoyl-phosphate synthetase 2, aspartate transcarbamylase and dihydroorotase (CAD), the first, rate-limiting enzyme in de novo pyrimidine biosynthesis. Through systematic mutational scanning and structural modelling, we find allostery as a major regulatory mechanism that controls the activity change of CAD during the cell cycle. Specifically, we report evidence of two Animalia-specific loops in the CAD allosteric domain that involve sensing and binding of uridine 5'-triphosphate, a CAD allosteric inhibitor. Based on homology with a mitochondrial carbamoyl-phosphate synthetase homologue, we identify a critical role for a signal transmission loop in regulating the formation of a substrate channel, thereby controlling CAD activity.
Collapse
Affiliation(s)
- Jong Shin
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Hannan Mir
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Maaz A Khurram
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Kenji M Fujihara
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Timothy J Cardozo
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Richard Possemato
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA.
| |
Collapse
|
149
|
Is ATP the Only Nucleoside Triphosphate among ATP, CTP, GTP, and UTP to Have a Role in Kinase Catalysis of Heme-Regulated Inhibitor toward eIF2α during Lung Cancer Development? Catalysts 2023. [DOI: 10.3390/catal13020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The heme-regulated eukaryotic initiation factor 2α (eIF2α) kinase, also known as heme-regulated inhibitor (HRI), detects misfolded proteins and induces cytoprotective response to stress, mainly caused by heme-shortage. The nucleoside triphosphate ATP serves as the main donor of phosphate for the phosphorylation of eIF2α by HRI in human cells. However, the other main nucleoside triphosphates (CTP, GTP, UTP) are also present at relatively high concentrations, especially in human tumor cells. Therefore, in this short communication we evaluate the role of four substrates (namely ATP, CTP, GTP, and UTP) on human HRI kinase activity. Additionally, for the first time, we perform a detailed kinetics study of the HRI G202S mutant, whose presence in the human lung is associated with cancer development. Here, the role of all four tested nucleoside triphosphates during cancer development is discussed from the point of view of the HRI activity. The results showed that the kcat value of GTP was lower than that of ATP but was significantly higher than those of CTP and UTP. Additionally, the kcat value of GTP for G202S was approximately 20% higher than that for wild-type, while the kcat values of ATP, CTP, and UTP for G202S were lower than those for wild-type.
Collapse
|
150
|
Boiarska Z, Pérez-Peña H, Abel AC, Marzullo P, Álvarez-Bernad B, Bonato F, Santini B, Horvath D, Lucena-Agell D, Vasile F, Sironi M, Díaz JF, Prota AE, Pieraccini S, Passarella D. Maytansinol Functionalization: Towards Useful Probes for Studying Microtubule Dynamics. Chemistry 2023; 29:e202203431. [PMID: 36468686 DOI: 10.1002/chem.202203431] [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: 11/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Maytansinoids are a successful class of natural and semisynthetic tubulin binders, known for their potent cytotoxic activity. Their wider application as cytotoxins and chemical probes to study tubulin dynamics has been held back by the complexity of natural product chemistry. Here we report the synthesis of long-chain derivatives and maytansinoid conjugates. We confirmed that bulky substituents do not impact their high activity or the scaffold's binding mode. These encouraging results open new avenues for the design of new maytansine-based probes.
Collapse
Affiliation(s)
- Zlata Boiarska
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Helena Pérez-Peña
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Anne-Catherine Abel
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Paola Marzullo
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Beatriz Álvarez-Bernad
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Francesca Bonato
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Benedetta Santini
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Dragos Horvath
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, 67081, Strasbourg, France
| | - Daniel Lucena-Agell
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Francesca Vasile
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Maurizio Sironi
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Stefano Pieraccini
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Daniele Passarella
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy
| |
Collapse
|