1
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Rutherford KA, McManus KJ. PROTACs: Current and Future Potential as a Precision Medicine Strategy to Combat Cancer. Mol Cancer Ther 2024; 23:454-463. [PMID: 38205881 PMCID: PMC10985480 DOI: 10.1158/1535-7163.mct-23-0747] [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: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Proteolysis targeting chimeras (PROTAC) are an emerging precision medicine strategy, which targets key proteins for proteolytic degradation to ultimately induce cancer cell killing. These hetero-bifunctional molecules hijack the ubiquitin proteasome system to selectively add polyubiquitin chains onto a specific protein target to induce proteolytic degradation. Importantly, PROTACs have the capacity to target virtually any intracellular and transmembrane protein for degradation, including oncoproteins previously considered undruggable, which strategically positions PROTACs at the crossroads of multiple cancer research areas. In this review, we present normal functions of the ubiquitin regulation proteins and describe the application of PROTACs to improve the efficacy of current broad-spectrum therapeutics. We subsequently present the potential for PROTACs to exploit specific cancer vulnerabilities through synthetic genetic approaches, which may expedite the development, translation, and utility of novel synthetic genetic therapies in cancer. Finally, we describe the challenges associated with PROTACs and the ongoing efforts to overcome these issues to streamline clinical translation. Ultimately, these efforts may lead to their routine clinical use, which is expected to revolutionize cancer treatment strategies, delay familial cancer onset, and ultimately improve the lives and outcomes of those living with cancer.
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Affiliation(s)
- Kailee A. Rutherford
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
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2
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William JNG, Dhar R, Gundamaraju R, Sahoo OS, Pethusamy K, Raj AFPAM, Ramasamy S, Alqahtani MS, Abbas M, Karmakar S. SKping cell cycle regulation: role of ubiquitin ligase SKP2 in hematological malignancies. Front Oncol 2024; 14:1288501. [PMID: 38559562 PMCID: PMC10978726 DOI: 10.3389/fonc.2024.1288501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
SKP2 (S-phase kinase-associated protein 2) is a member of the F-box family of substrate-recognition subunits in the SCF ubiquitin-protein ligase complexes. It is associated with ubiquitin-mediated degradation in the mammalian cell cycle components and other target proteins involved in cell cycle progression, signal transduction, and transcription. Being an oncogene in solid tumors and hematological malignancies, it is frequently associated with drug resistance and poor disease outcomes. In the current review, we discussed the novel role of SKP2 in different hematological malignancies. Further, we performed a limited in-silico analysis to establish the involvement of SKP2 in a few publicly available cancer datasets. Interestingly, our study identified Skp2 expression to be altered in a cancer-specific manner. While it was found to be overexpressed in several cancer types, few cancer showed a down-regulation in SKP2. Our review provides evidence for developing novel SKP2 inhibitors in hematological malignancies. We also investigated the effect of SKP2 status on survival and disease progression. In addition, the role of miRNA and its associated families in regulating Skp2 expression was explored. Subsequently, we predicted common miRNAs against Skp2 genes by using miRNA-predication tools. Finally, we discussed current approaches and future prospective approaches to target the Skp2 gene by using different drugs and miRNA-based therapeutics applications in translational research.
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Affiliation(s)
- Jonahunnatha Nesson George William
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), Ageing Research Center and Translational Medicine-CeSI-MeT, “G. d’Annunzio” University Chieti-Pescara, Chieti, Italy
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Intestinal Mucosal Biology Lab, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Om Saswat Sahoo
- Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease Laboratory, Department Of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, University of Leicester, Leicester, United Kingdom
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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3
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Bhattacharya A, Shukla VK, Kachariya N, Preeti, Sehrawat P, Kumar A. Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly. J Mol Biol 2022; 434:167830. [PMID: 36116539 DOI: 10.1016/j.jmb.2022.167830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/20/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Skp1(S-phase kinase-associated protein 1 - Homo sapiens) is an adapter protein of the SCF(Skp1-Cullin1-Fbox) complex, which links the constant components (Cul1-RBX) and the variable receptor (F-box proteins) in Ubiquitin E3 ligase. It is intriguing how Skp1 can recognise and bind to a variety of structurally different F-box proteins. For practical reasons, previous efforts have used truncated Skp1, and thus it has not been possible to track the crucial aspects of the substrate recognition process. In this background, we report the solution structure of the full-length Skp1 protein determined by NMR spectroscopy for the first time and investigate the sequence-dependent dynamics in the protein. The solution structure reveals that Skp1 has an architecture: β1-β2-H1-H2-L1-H3-L2-H4-H5-H6-H7(partially formed) and a long tail-like disordered C-terminus. Structural analysis using DALI (Distance Matrix Alignment) reveals conserved domain structure across species for Skp1. Backbone dynamics investigated using NMR relaxation suggest substantial variation in the motional timescales along the length of the protein. The loops and the C-terminal residues are highly flexible, and the (R2/R1) data suggests μs-ms timescale motions in the helices as well. Further, the dependence of amide proton chemical shift on temperature and curved profiles of their residuals indicate that the residues undergo transitions between native state and excited state. The curved profiles for several residues across the length of the protein suggest that there are native-like low-lying excited states, particularly for several C-terminal residues. Our results provide a rationale for how the protein can adapt itself, bind, and get functionally associated with other proteins in the SCF complex by utilising its flexibility and conformational sub-states.
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Affiliation(s)
- Amrita Bhattacharya
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vaibhav Kumar Shukla
- Biophysical Chemistry & Structural Biology Laboratory, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India. https://twitter.com/bhu_vaibhav
| | - Nitin Kachariya
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Preeti
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Parveen Sehrawat
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ashutosh Kumar
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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4
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Hussain M, Lu Y, Tariq M, Jiang H, Shu Y, Luo S, Zhu Q, Zhang J, Liu J. A small-molecule Skp1 inhibitor elicits cell death by p53-dependent mechanism. iScience 2022; 25:104591. [PMID: 35789855 PMCID: PMC9249674 DOI: 10.1016/j.isci.2022.104591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Skp1 overexpression promotes tumor growth, whereas reduced Skp1 activity is also linked with genomic instability and neoplastic transformation. This highlights the need to gain better understanding of Skp1 biology in cancer settings. To this context, potent and cellularly active small-molecule Skp1 inhibitors may be of great value. Using a hypothesis-driven, structure-guided approach, we herein identify Z0933M as a potent Skp1 inhibitor with KD ∼0.054 μM. Z0933M occupies a hydrophobic hotspot (P1) – encompassing an aromatic cage of two phenylalanines (F101 and F139) – alongside C-terminal extension of Skp1 and, thus, hampers its ability to interact with F-box proteins, a prerequisite step to constitute intact and active SCF E3 ligase(s) complexes. In cellulo, Z0933M disrupted SCF E3 ligase(s) functioning, recapitulated previously reported effects of Skp1-reduced activity, and elicited cell death by a p53-dependent mechanism. We propose Z0933M as valuable tool for future efforts toward probing Skp1 cancer biology, with implications for cancer therapy. Z0933M manifests strong binding with Skp1 and inhibits Skp1-F-box PPIs Z0933M interacts with a P1 hotspot alongside C-terminal extension of Skp1 Z0933M alters SCF E3 ligase functioning, leading to substrate accumulation/modulation Z0933M causes cell-cycle arrest, and elicits cell death by p53-dependent mechanism
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Affiliation(s)
- Muzammal Hussain
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongzhi Lu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Muqddas Tariq
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Hao Jiang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Yahai Shu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Shuang Luo
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Jiancun Zhang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Corresponding author
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5
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Hu K, Li XJ, Asmamaw MD, Shi XJ, Liu HM. Establishment of high-throughput screening HTRF assay for identification small molecule inhibitors of Skp2-Cks1. Sci Rep 2021; 11:21105. [PMID: 34702937 PMCID: PMC8548536 DOI: 10.1038/s41598-021-00646-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
S-phase kinase associated protein 2 (Skp2), a member of the F-box family that constitute the largest known class of ubiquitin E3 specificity components, is responsible for recognizing and recruiting cyclin-dependent kinase inhibitor p27 for its ubiquitination in the presence of the small accessory protein cyclin-dependent kinase regulatory subunit 1(Cks1). Skp2 is overexpressed in esophageal carcinoma tissues and closely related with tumor poor prognosis, and perturbation of the Skp2-Cks1 interaction by inhibitors or RNAi could inhibit the proliferation and metastasis of tumor cells. Therefore, inhibition of Skp2 function by small-molecule compounds targeting Skp2-Cks1 interaction is emerging as a promising and novel anti-cancer strategy. In this study, we establish an improved high-throughput screening platform to screen Skp2 inhibitors targeting Skp2-Cks1interaction, which may provide a new therapeutic approach for the clinic.
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Affiliation(s)
- Kaizhao Hu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control and Evaluation, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiao-Jing Li
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control and Evaluation, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Moges Dessale Asmamaw
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control and Evaluation, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiao-Jing Shi
- Laboratory Animal Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan Province, China.
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control and Evaluation, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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6
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Thompson LL, Rutherford KA, Lepage CC, McManus KJ. The SCF Complex Is Essential to Maintain Genome and Chromosome Stability. Int J Mol Sci 2021; 22:8544. [PMID: 34445249 PMCID: PMC8395177 DOI: 10.3390/ijms22168544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
The SKP1, CUL1, F-box protein (SCF) complex encompasses a group of 69 SCF E3 ubiquitin ligase complexes that primarily modify protein substrates with poly-ubiquitin chains to target them for proteasomal degradation. These SCF complexes are distinguishable by variable F-box proteins, which determine substrate specificity. Although the function(s) of each individual SCF complex remain largely unknown, those that have been characterized regulate a wide array of cellular processes, including gene transcription and the cell cycle. In this regard, the SCF complex regulates transcription factors that modulate cell signaling and ensures timely degradation of primary cell cycle regulators for accurate replication and segregation of genetic material. SCF complex members are aberrantly expressed in a myriad of cancer types, with altered expression or function of the invariable core SCF components expected to have a greater impact on cancer pathogenesis than that of the F-box proteins. Accordingly, this review describes the normal roles that various SCF complexes have in maintaining genome stability before discussing the impact that aberrant SCF complex expression and/or function have on cancer pathogenesis. Further characterization of the SCF complex functions is essential to identify and develop therapeutic approaches to exploit aberrant SCF complex expression and function.
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Affiliation(s)
- Laura L. Thompson
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kailee A. Rutherford
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Chloe C. Lepage
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kirk J. McManus
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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7
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Thompson LL, Baergen AK, Lichtensztejn Z, McManus KJ. Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover. Cancers (Basel) 2020; 12:E531. [PMID: 32106628 PMCID: PMC7139525 DOI: 10.3390/cancers12030531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome instability (CIN), or progressive changes in chromosome numbers, is an enabling feature of many cancers; however, the mechanisms giving rise to CIN remain poorly understood. To expand our mechanistic understanding of the molecular determinants of CIN in humans, we employed a cross-species approach to identify 164 human candidates to screen. Using quantitative imaging microscopy (QuantIM), we show that silencing 148 genes resulted in significant changes in CIN-associated phenotypes in two distinct cellular contexts. Ten genes were prioritized for validation based on cancer patient datasets revealing frequent gene copy number losses and associations with worse patient outcomes. QuantIM determined silencing of each gene-induced CIN, identifying novel roles for each as chromosome stability genes. SKP1 was selected for in-depth analyses as it forms part of SCF (SKP1, CUL1, FBox) complex, an E3 ubiquitin ligase that targets proteins for proteolytic degradation. Remarkably, SKP1 silencing induced increases in replication stress, DNA double strand breaks and chromothriptic events that were ascribed to aberrant increases in Cyclin E1 levels arising from reduced SKP1 expression. Collectively, these data reveal a high degree of evolutionary conservation between human and budding yeast CIN genes and further identify aberrant mechanisms associated with increases in chromothriptic events.
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Affiliation(s)
- Laura L. Thompson
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Allison K. Baergen
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Kirk J. McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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8
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Lough L, Sherman D, Ni E, Young LM, Hao B, Cardozo T. Chemical probes of Skp2-mediated p27 ubiquitylation and degradation. MEDCHEMCOMM 2018; 9:1093-1104. [PMID: 30108998 DOI: 10.1039/c8md00140e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/05/2018] [Indexed: 12/16/2022]
Abstract
Skp2 is a member of the F-box family of proteins that serve as substrate-specific adaptors in Skp1-CUL1-ROC1-F-box (SCF) E3 ubiquitin ligases. Skp2 (Fbxl1) directly binds to the tumor suppressor p27 in the context of the SCFSkp2 E3 ubiquitin ligase to ubiquitylate and target-phosphorylated p27 for proteasomal degradation. As p27 is a powerful suppressor of growth in a variety of cells, and as Skp2 is also overexpressed in many human cancers, Skp2 is considered an oncogene and an intriguing drug target. However, despite 20 years of investigation, a valid chemical inhibitor of Skp2-mediated degradation of p27 has not been identified. Recently, an increasing number of compounds designed to have this bioactivity have been reported. Here, we conduct a meta-analysis of the evidence regarding bioactivity, structure, and medicinal chemistry in order to evaluate and compare these Skp2 inhibitor compounds. Despite chemically diverse compounds with a wide array of Skp2-mediated p27 ubiquitylation inhibition properties reported by several independent groups, no current chemical probe formally qualifies as a validated pharmaceutical hit compound. This finding suggests that our knowledge of the structural biochemistry of the Skp2-p27 complex remains incomplete and highlights the need for novel modes of inquiry.
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Affiliation(s)
- Lea Lough
- Department of Biochemistry and Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA . ; ; Tel: +1 212 263 6337
| | - Dan Sherman
- Department of Biochemistry and Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA . ; ; Tel: +1 212 263 6337
| | - Eric Ni
- Department of Biochemistry and Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA . ; ; Tel: +1 212 263 6337
| | - Lauren M Young
- Department of Biochemistry and Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA . ; ; Tel: +1 212 263 6337
| | - Bing Hao
- Department of Molecular Biology and Biophysics , University of Connecticut Health Center , Farmington , CT 06030 , USA
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA . ; ; Tel: +1 212 263 6337
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9
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Xu X, Eletsky A, Sheikh MO, Prestegard JH, West CM. Glycosylation Promotes the Random Coil to Helix Transition in a Region of a Protist Skp1 Associated with F-Box Binding. Biochemistry 2017; 57:511-515. [PMID: 29251491 DOI: 10.1021/acs.biochem.7b01033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cullin-ring-ligases mediate protein polyubiquitination, a signal for degradation in the 26S proteasome. The CRL1 class consists of Skp1/cullin-1/F-box protein/Rbx1 (SCF) complexes that cyclically associate with ubiquitin-E2 to build the polyubiquitin chain. Within the SCF complex, the 162-amino acid DdSkp1 from Dictyostelium bridges cullin-1 with an F-box protein (FBP), the specificity factor for substrate selection. The hydroxylation-dependent glycosylation of Pro143 of DdSkp1 by a pentasaccharide forms the basis of a novel O2-sensing mechanism in the social amoeba Dictyostelium and other protists. Previous evidence indicated that glycosylation promotes increased α-helical content correlating with enhanced interaction with three F-box proteins. To localize these differences, we used nuclear magnetic resonance (NMR) methods to compare nonglycosylated DdSkp1 and a glycoform with a single GlcNAc sugar (Gn-DdSkp1). We report NMR assignments of backbone 1HN, 15N, 13Cα, and 13CO nuclei as well as side-chain 13Cβ and methyl 13C/1H nuclei of Ile(δ1), Leu, and Val in both unmodified DdSkp1 and Gn-DdSkp1. The random coil index and 15N{1H} HNOE indicate that the C-terminal region, which forms a helix-loop-helix motif centered on Pro143 at the crystallographically defined binding interface with F-box domains, remains dynamic in both DdSkp1 and Gn-DdSkp1. Chemical shifts indicate that the variation of conformation in Gn-DdSkp1, relative to DdSkp1, is limited to this region and characterized by increased helical fold. Extension of the glycan chain results in further changes, also limited to this region. Thus, glycosylation may control F-box protein interactions via a local effect on DdSkp1 conformation, by a mechanism that may be general to many unicellular eukaryotes.
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Affiliation(s)
- Xianzhong Xu
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Alexander Eletsky
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - M Osman Sheikh
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - James H Prestegard
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Christopher M West
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
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10
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Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM. O 2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J Biol Chem 2017; 292:18897-18915. [PMID: 28928219 PMCID: PMC5704474 DOI: 10.1074/jbc.m117.809160] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a conserved protein linking cullin-1 to F-box proteins in SCF (Skp1/Cullin-1/F-box protein) E3 ubiquitin ligases, which modify protein substrates with polyubiquitin chains that typically target them for 26S proteasome-mediated degradation. In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. Previous studies have shown that the glycan promotes organization of the F-box-binding region in Skp1 and aids in Skp1's association with F-box proteins. Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. Molecular dynamics trajectories of glycosylated Skp1 whose calculated monosaccharide relaxation kinetics and rotational correlation times agreed with the NMR data indicated that the glycan interacts with the loop connecting two α-helices of the F-box-combining site. In these trajectories, the helices separated from one another to create a more accessible and dynamic F-box interface. These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. The increased sampling of an open Skp1 conformation can explain how glycosylation enhances interactions with F-box proteins in cells.
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Affiliation(s)
- M Osman Sheikh
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | - Gordon Chalmers
- the Complex Carbohydrate Research Center, and
- the Department of Computer Science, University of Georgia, Athens, Georgia 30602
| | - Christopher M Schafer
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | | | - Robert J Woods
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | | | - Brad Bendiak
- the Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James H Prestegard
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology,
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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11
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Tao T, Zhou CJ, Wang Q, Chen XR, Sun Q, Zhao TY, Ye JC, Wang Y, Zhang ZY, Zhang YL, Guo ZJ, Wang XB, Li DW, Yu JL, Han CG. Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway. PLoS One 2017; 12:e0177518. [PMID: 28494021 PMCID: PMC5426791 DOI: 10.1371/journal.pone.0177518] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/29/2017] [Indexed: 11/18/2022] Open
Abstract
As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.
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Affiliation(s)
- Tao Tao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Cui-Ji Zhou
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong Province, People's Republic of China
| | - Xiang-Ru Chen
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Qian Sun
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Tian-Yu Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Jian-Chun Ye
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Ying Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Zong-Ying Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Yong-Liang Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Ze-Jian Guo
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Xian-Bing Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Da-Wei Li
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Jia-Lin Yu
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Cheng-Gui Han
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
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12
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Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
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Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
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13
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Kachariya NN, Dantu SC, Kumar A. Backbone and side chain assignments of human cell cycle regulatory protein S-phase kinase-associated protein 1. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:351-355. [PMID: 27394725 DOI: 10.1007/s12104-016-9699-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/02/2016] [Indexed: 06/06/2023]
Abstract
Ubiquitination of proteins is required to regulate several cellular mechanisms in cells. Skp1-Cullin-1-F-box (SCF), the largest family of the RING E3 ligases, recognizes and carries out the poly-ubiquitination of many substrate proteins. SCF E3 ligase is a multi-component protein complex, and the human S-phase kinase-associated protein 1 (Skp1) is the adapter protein, which binds and presents the substrate binding protein F-box (FBP) to the rest of the E3 ligase. Several crystallographic studies have solved the partial structure of Skp1 in complex with various FBPs, but there is no structure of standalone Skp1. Understanding the conformational and structural properties of Skp1 with and without FBPs is required to understand the complete mechanism of poly-ubiquitination. Here, we report ~90 % backbone and 64 % side chain (1)H, (13)C, (15)N assignments of Skp1 protein using various double and triple resonance NMR experiments.
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Affiliation(s)
- Nitin Nathubhai Kachariya
- Room No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sarath Chandra Dantu
- Room No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ashutosh Kumar
- Room No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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14
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Dhaked HPS, Bhattacharya A, Yadav S, Dantu SC, Kumar A, Panda D. Mutation of Arg191 in FtsZ Impairs Cytokinetic Abscission of Bacillus subtilis Cells. Biochemistry 2016; 55:5754-5763. [DOI: 10.1021/acs.biochem.6b00493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hemendra Pal Singh Dhaked
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Anusri Bhattacharya
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Saroj Yadav
- IITB-Monash
Research Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sarath Chandra Dantu
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ashutosh Kumar
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dulal Panda
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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15
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Dantu SC, Khavnekar S, Kale A. Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study. J Biomol Struct Dyn 2016; 35:2186-2196. [DOI: 10.1080/07391102.2016.1209131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sarath Chandra Dantu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sagar Khavnekar
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
| | - Avinash Kale
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
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