1
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Talati VP, Karn V, Gadewal N, Bastikar VA. Mechanistic influence of discreet conformation of human telomerase linker region. J Biomol Struct Dyn 2024:1-8. [PMID: 38319038 DOI: 10.1080/07391102.2024.2310212] [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: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Approximately 90% of malignancies have been shown to have human telomerase activity, establishing it as a viable therapeutic target. The crystal structure of telomerase was determined recently. However, the tertiary structure of the non-conserved flexible linker region remains unresolved. This study aims to predict the full-length tertiary structure of the human telomerase reverse transcriptase (hTERT). Two strategies were employed to determine the full-length structure of hTERT (1132 amino acids); iterative threading and a conjoined model generated from machine learning and energy functions. After energy minimization, Ramachandran Plot analysis, and simulation; the conjoined model was considered of better quality and stability. The linker region of the conjoined depicted two helices from approximately 275-284 and 201-211 amino acids respectively in contrast to the iterative threading model which has a single helix. Moreover, the region was observed to undergo major structural changes throughout the simulation. These changes signify its flexibility which might be due to the region having a significant number of glycine and proline and could enhance the clamping movement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varun P Talati
- Amity Institute of Biotechnology, Amity University Mumbai, Mumbai, Maharashtra, India
| | - Vamika Karn
- Amity Institute of Biotechnology, Amity University Mumbai, Mumbai, Maharashtra, India
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai, Maharashtra, India
| | - Virupaksha A Bastikar
- Amity Institute of Biotechnology, Amity University Mumbai, Mumbai, Maharashtra, India
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2
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Aureli S, Cardenas VB, Raniolo S, Limongelli V. Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase. Commun Chem 2023; 6:242. [PMID: 37935941 PMCID: PMC10630336 DOI: 10.1038/s42004-023-01040-y] [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: 02/27/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
The Shelterin complex protein TPP1 interacts with human telomerase (TERT) by means of the TEL-patch region, controlling telomere homeostasis. Aberrations in the TPP1-TERT heterodimer formation might lead to short telomeres and severe diseases like dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. In the present study, we provide a thorough characterization of the structural properties of the TPP1's OB-domain by combining data coming from microsecond-long molecular dynamics calculations, time-series analyses, and graph-based networks. Our results show that the TEL-patch conformational freedom is influenced by a network of long-range amino acid communications that together determine the proper TPP1-TERT binding. Furthermore, we reveal that in TPP1 pathological variants Glu169Δ, Lys170Δ and Leu95Gln, the TEL-patch plasticity is reduced, affecting the correct binding to TERT and, in turn, telomere processivity, which eventually leads to accelerated aging of affected cells. Our study provides a structural basis for the design of TPP1-targeting ligands with therapeutic potential against cancer and telomeropathies.
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Affiliation(s)
- Simone Aureli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneve, Rue Michel-Servet 1, Geneva, CH-1211, Switzerland
- Swiss Institute of Bioinformatics, University of Geneve, Geneva, CH-1206, Switzerland
| | - Vince Bart Cardenas
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
| | - Stefano Raniolo
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland.
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3
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Idrees M, Kumar V, Khan AM, Joo MD, Lee KW, Sohn SH, Kong IK. Cycloastragenol activation of telomerase improves β-Klotho protein level and attenuates age-related malfunctioning in ovarian tissues. Mech Ageing Dev 2023; 209:111756. [PMID: 36462538 DOI: 10.1016/j.mad.2022.111756] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Age-related deterioration in the reproductive capacity of women is directly related to the poor developmental potential of ovarian follicles. Although telomerase plays a key role in female fertility, TERT-targeting therapeutic strategies for age-related female infertility have yet to be investigated. This study elucidated the effect of Telomerase activation on mice ovaries and more specifically on Klb (β-Klotho) gene expression, which is linked to ageing, female hormonal regulation, and cyclicity. The homology-based 3D model of hTERT was used to predict its binding mode of Cycloastragenol (CAG) using molecular docking and molecular dynamics simulations. Based on docking score, simulation behavior, and interaction with hTERT residues it was observed that CAG could bind with the hTERT model. CAG treatment to primary cultured mouse granulosa cells and activation of telomerase was examined via telomerase activity assay (Mouse TE (telomerase) ELISA Kit) and telomere length by quantitative fluorescence in situ hybridization. CAG mediated telomerase also significantly improved β-Klotho protein level in the aged granulosa cells. To demonstrate that β-Klotho is telomerase dependent, the TERT was knocked down via siRNA in granulosa cells and protein level of β-Klotho was examined. Furthermore, CAG-mediated telomerase activation significantly enhanced the level of Klb and recovered ovarian follicles in the D-galactose (D-gal)-induced ovarian ageing mouse model. Moreover, Doxorubicin-induced ovarian damage, which changes ovarian hormones, and inhibit follicular growth was successfully neutralized by CAG activated telomerase and its recovery of β-Klotho level. In conclusion, TERT dependent β-Klotho regulation in ovarian tissues is one of the mechanisms, which can overcome female infertility.
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Affiliation(s)
- Muhammad Idrees
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Republic of Korea.
| | - Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - Abdul Majid Khan
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Republic of Korea.
| | - Myeong-Don Joo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Republic of Korea.
| | - Keun-Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - Sea-Hwan Sohn
- Department of Animal Science and Biotechnology, Gyeongsang National University, Jinju 52725, Gyeongnam Province, Republic of Korea.
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Republic of Korea; Institute of Agriculture and Life Science, Gyeongsang National University, Gyeongnam Province, Republic of Korea; The King Kong Corp. Ltd., Gyeongsang National University, Jinju 52828, Gyeongnam Province, Republic of Korea.
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4
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Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD. Mechanisms of nucleotide selection by telomerase. eLife 2020; 9:55438. [PMID: 32501800 PMCID: PMC7274783 DOI: 10.7554/elife.55438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/18/2020] [Indexed: 01/31/2023] Open
Abstract
Telomerase extends telomere sequences at chromosomal ends to protect genomic DNA. During this process it must select the correct nucleotide from a pool of nucleotides with various sugars and base pairing properties, which is critically important for the proper capping of telomeric sequences by shelterin. Unfortunately, how telomerase selects correct nucleotides is unknown. Here, we determined structures of Tribolium castaneum telomerase reverse transcriptase (TERT) throughout its catalytic cycle and mapped the active site residues responsible for nucleoside selection, metal coordination, triphosphate binding, and RNA template stabilization. We found that TERT inserts a mismatch or ribonucleotide ~1 in 10,000 and ~1 in 14,000 insertion events, respectively. At biological ribonucleotide concentrations, these rates translate to ~40 ribonucleotides inserted per 10 kilobases. Human telomerase assays determined a conserved tyrosine steric gate regulates ribonucleotide insertion into telomeres. Cumulatively, our work provides insight into how telomerase selects the proper nucleotide to maintain telomere integrity.
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Affiliation(s)
- Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Griffin A Welfer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, United States
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5
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Bajaj S, Kumar MS, Peters GJ, Mayur YC. Targeting telomerase for its advent in cancer therapeutics. Med Res Rev 2020; 40:1871-1919. [PMID: 32391613 DOI: 10.1002/med.21674] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022]
Abstract
Telomerase has emerged as an important primary target in anticancer therapy. It is a distinctive reverse transcriptase enzyme, which extends the length of telomere at the 3' chromosomal end, and uses telomerase reverse transcriptase (TERT) and telomerase RNA template-containing domains. Telomerase has a vital role and is a contributing factor in human health, mainly affecting cell aging and cell proliferation. Due to its unique feature, it ensures unrestricted cell proliferation in malignancy and plays a major role in cancer disease. The development of telomerase inhibitors with increased specificity and better pharmacokinetics is being considered to design and develop newer potent anticancer agents. Use of natural and synthetic compounds for the inhibition of telomerase activity can lead to an opening of new vistas in cancer treatment. This review details about the telomerase biochemistry, use of natural and synthetic compounds; vaccines and oncolytic virus in therapy that suppress the telomerase activity. We have discussed structure-activity relationships of various natural and synthetic telomerase inhibitors to help medicinal chemists and chemical biology researchers with a ready reference and updated status of their clinical trials. Suppression of human TERT (hTERT) activity through inhibition of hTERT promoter is an important approach for telomerase inhibition.
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Affiliation(s)
| | | | - G J Peters
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Y C Mayur
- SPPSPTM, SVKM's NMIMS, Mumbai, India
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6
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Baginski M, Serbakowska K. In silico design of telomerase inhibitors. Drug Discov Today 2020; 25:1213-1222. [PMID: 32387261 DOI: 10.1016/j.drudis.2020.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022]
Abstract
Telomerase is a reverse transcriptase enzyme involved in DNA synthesis at the end of linear chromosomes. Unlike in most other cells, telomerase is reactivated most cancerous cells and, therefore, has become a promising new anticancer target. Despite extensive research, direct telomerase inhibitors have yet not been introduced to the clinics because of the complexity of this enzyme. Structures of this protein from simple organisms and human homology models are currently available and have been used in structure-based drug design efforts to find potential inhibitors. Different is silico strategies have been applied and different chemical groups have been explored. Here, we provide an overview of recent discoveries.
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Affiliation(s)
- Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland.
| | - Katarzyna Serbakowska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland
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7
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Tutone M, Pecoraro B, Almerico AM. Investigation on Quantitative Structure-Activity Relationships of 1,3,4-Oxadiazole Derivatives as Potential Telomerase Inhibitors. Curr Drug Discov Technol 2020; 17:79-86. [PMID: 30039762 DOI: 10.2174/1570163815666180724113208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Telomerase, a reverse transcriptase, maintains telomere and chromosomes integrity of dividing cells, while it is inactivated in most somatic cells. In tumor cells, telomerase is highly activated, and works in order to maintain the length of telomeres causing immortality, hence it could be considered as a potential marker to tumorigenesis.A series of 1,3,4-oxadiazole derivatives showed significant broad-spectrum anticancer activity against different cell lines, and demonstrated telomerase inhibition. METHODS This series of 24 N-benzylidene-2-((5-(pyridine-4-yl)-1,3,4-oxadiazol-2yl)thio)acetohydrazide derivatives as telomerase inhibitors has been considered to carry out QSAR studies. The endpoint to build QSAR models is determined by the IC50 values for telomerase inhibition, i.e., the concentration (μM) of inhibitor that produces 50% inhibition. These values were converted to pIC50 (- log IC50) values. We used the most common and transparent method, where models are described by clearly expressed mathematical equations: Multiple Linear Regression (MLR) by Ordinary Least Squares (OLS). RESULTS Validated models with high correlation coefficients were developed. The Multiple Linear Regression (MLR) models, by Ordinary Least Squares (OLS), showed good robustness and predictive capability, according to the Multi-Criteria Decision Making (MCDM = 0.8352), a technique that simultaneously enhances the performances of a certain number of criteria. The descriptors selected for the models, such as electrotopological state (E-state) descriptors, and extended topochemical atom (ETA) descriptors, showed the relevant chemical information contributing to the activity of these compounds. CONCLUSION The results obtained in this study make sure about the identification of potential hits as prospective telomerase inhibitors.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Universita degli Studi di Palermo, via Archirafi 28, 90123-Palermo, Italy
| | - Beatrice Pecoraro
- Department of Clinical and Pharmaceutical Sciences, School of Life and Medical Sciences, University of Hertfordshire, College Lane, Hatfield, Hertfordshire AL10 9AB, United Kingdom
| | - Anna M Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Universita degli Studi di Palermo, via Archirafi 28, 90123-Palermo, Italy
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8
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Jansson LI, Stone MD. Single-Molecule Analysis of Reverse Transcriptase Enzymes. Cold Spring Harb Perspect Biol 2019; 11:11/9/a032458. [PMID: 31481455 DOI: 10.1101/cshperspect.a032458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The original discovery of enzymes that synthesize DNA using an RNA template appeared to contradict the central dogma of biology, in which information is transferred, in a unidirectional way, from DNA genes into RNA molecules. The paradigm-shifting discovery of RNA-dependent DNA polymerases, also called reverse transcriptases (RTs), reshaped existing views for how cells function; however, the scope of the impact RTs impose on biology had yet to be realized. In the decades of research since the early 1970s, the biomedical and biotechnological significance of retroviral RTs, as well as the evolutionarily related telomerase enzyme, has become exceedingly clear. One common theme that has emerged in the course of RT-related research is the central role of nucleic acid binding and dynamics during enzyme function. However, directly interrogating these dynamic properties is challenging because of the stochastic properties of biological macromolecules. In this review, we describe how the development of single-molecule biophysical techniques has opened new windows through which to observe the dynamic behavior of this remarkable class of enzymes. Specifically, we focus on how the powerful single-molecule Förster resonance energy transfer (FRET) method has been exploited to study the structure and function of the human immunodeficiency virus (HIV) RT and telomerase ribonucleoprotein (RNP) enzymes. These exciting studies have refined our understanding of RT catalysis, have revealed unforeseen structural rearrangements between RTs and their nucleic acid substrates, and have helped to characterize the mode of action of RT-inhibiting drugs. We conclude with a discussion of how the ongoing development of single-molecule technologies will continue to empower researchers to probe RT mechanisms in new and exciting ways.
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Affiliation(s)
- Linnea I Jansson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
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9
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Petrova OA, Mantsyzov AB, Rodina EV, Efimov SV, Hackenberg C, Hakanpää J, Klochkov VV, Lebedev AA, Chugunova AA, Malyavko AN, Zatsepin TS, Mishin AV, Zvereva MI, Lamzin VS, Dontsova OA, Polshakov VI. Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase. Nucleic Acids Res 2019; 46:1525-1540. [PMID: 29294091 PMCID: PMC5814841 DOI: 10.1093/nar/gkx1275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022] Open
Abstract
The elongation of single-stranded DNA repeats at the 3′-ends of chromosomes by telomerase is a key process in maintaining genome integrity in eukaryotes. Abnormal activation of telomerase leads to uncontrolled cell division, whereas its down-regulation is attributed to ageing and several pathologies related to early cell death. Telomerase function is based on the dynamic interactions of its catalytic subunit (TERT) with nucleic acids—telomerase RNA, telomeric DNA and the DNA/RNA heteroduplex. Here, we present the crystallographic and NMR structures of the N-terminal (TEN) domain of TERT from the thermotolerant yeast Hansenula polymorpha and demonstrate the structural conservation of the core motif in evolutionarily divergent organisms. We identify the TEN residues that are involved in interactions with the telomerase RNA and in the recognition of the ‘fork’ at the distal end of the DNA product/RNA template heteroduplex. We propose that the TEN domain assists telomerase biological function and is involved in restricting the size of the heteroduplex during telomere repeat synthesis.
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Affiliation(s)
- Olga A Petrova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey B Mantsyzov
- Centre for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena V Rodina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sergey V Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya, Kazan 420008, Russia
| | - Claudia Hackenberg
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Vladimir V Klochkov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya, Kazan 420008, Russia
| | - Andrej A Lebedev
- Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, UK
| | - Anastasia A Chugunova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander N Malyavko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Timofei S Zatsepin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey V Mishin
- Laboratory for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria I Zvereva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Victor S Lamzin
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Olga A Dontsova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vladimir I Polshakov
- Centre for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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10
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations. Sci Rep 2019; 9:8707. [PMID: 31213647 PMCID: PMC6581908 DOI: 10.1038/s41598-019-45206-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022] Open
Abstract
Overexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation, or directly affecting its enzymatic activity. In this work, potential human telomerase mutations were identified by a systematic computational approach. Moreover, molecular docking methods were used to predict the effects of these mutations on the affinity of certain ligands (C_9i, C_9k, 16A, and NSC749234). The C_9k inhibitor had the best binding affinity for wild-type (WT) telomerase. Moreover, C_9i and C_9k had improved interactions with human telomerase in most of the mutant models. The R631 and Y717 residues of WT telomerase formed interactions with all studied ligands and these interactions were also commonly found in most of the mutant models. Residues forming stable interactions with ligands in molecular dynamics (MD) were traced, and the MD simulations showed that the C_9k ligand formed different conformations with WT telomerase than the C_9i ligand.
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11
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Lv Z, Li C, Guo M, Shao Y, Zhang W, Zhao X. Major yolk protein and HSC70 are essential for the activation of the TLR pathway via interacting with MyD88 in Apostichopus japonicus. Arch Biochem Biophys 2019; 665:57-68. [DOI: 10.1016/j.abb.2019.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022]
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12
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Herrera FE, Sferco SJ. Human telomerase protein: Understanding how the catalytic activity is suppressed under single substitutions of some conserved residues. A computational study. Proteins 2018; 86:1020-1036. [DOI: 10.1002/prot.25573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/05/2018] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Fernando E. Herrera
- Physics Department, Facultad de Bioquímica y Ciencias Biológicas; Universidad Nacional del Litoral. Ciudad Universitaria; Santa Fe Argentina
| | - Silvano J. Sferco
- Physics Department, Facultad de Bioquímica y Ciencias Biológicas; Universidad Nacional del Litoral. Ciudad Universitaria; Santa Fe Argentina
- Instituto de Física del Litoral (IFIS Litoral, UNL-CONICET); Santa Fe Argentina
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13
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Jin Y, You L, Kim HJ, Lee HW. Telomerase Reverse Transcriptase Contains a BH3-Like Motif and Interacts with BCL-2 Family Members. Mol Cells 2018; 41:684-694. [PMID: 29937479 PMCID: PMC6078858 DOI: 10.14348/molcells.2018.0206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022] Open
Abstract
Upregulation of human telomerase reverse transcriptase (hTERT) expression is an important factor in the cellular survival and cancer. Although growing evidence suggests that hTERT inhibits cellular apoptosis by telomere-independent functions, the mechanisms involved are not fully understood. Here, we show that hTERT contains a BH3-like motif, a short peptide sequence found in BCL-2 family proteins, and interacts with anti-apoptotic BCL-2 family proteins MCL-1 and BCL-xL, suggesting a functional link between hTERT and the mitochondrial pathway of apoptosis. Additionally, we propose that hTERT can be categorized into the atypical BH3-only proteins that promote cellular survival, possibly due to the non-canonical interaction between hTERT and antiapoptotic proteins. Although the detailed mechanisms underlying the hTERT BH3-like motif functions and interactions between hTERT and BCL-2 family proteins have not been elucidated, this work proposes a possible connection between hTERT and BCL-2 family members and reconsiders the role of the BH3-like motif as an interaction motif.
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Affiliation(s)
- Young Jin
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
| | - Long You
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
| | - Hye Jeong Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
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14
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Kazemi Noureini S, Kheirabadi M, Masoumi F, Khosrogerdi F, Zarei Y, Suárez-Rozas C, Salas-Norambuena J, Kennedy Cassels B. Telomerase Inhibition by a New Synthetic Derivative of the Aporphine Alkaloid Boldine. Int J Mol Sci 2018; 19:ijms19041239. [PMID: 29671783 PMCID: PMC5979471 DOI: 10.3390/ijms19041239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Telomerase, the enzyme responsible for cell immortality, is an important target in anti-cancer drug discovery. Boldine, an abundant aporphine alkaloid of Peumus boldus, is known to inhibit telomerase at non-toxic concentrations. Cytotoxicity of N-benzylsecoboldine hydrochloride (BSB), a synthetic derivative of boldine, was determined using the MTT method in MCF7 and MDA-MB231 cells. Aliquots of cell lysates were incubated with various concentrations of BSB in qTRAP (quantitative telomere repeat amplification protocol)-ligand experiments before substrate elongation by telomerase or amplification by hot-start Taq polymerase. The crystal structure of TERT, the catalytic subunit of telomerase from Tribolium castaneum, was used for docking and molecular dynamics analysis. The qTRAP-ligand data gave an IC50 value of about 0.17 ± 0.1 µM for BSB, roughly 400 times stronger than boldine, while the LD50 in the cytotoxicity assays were 12.5 and 21.88 µM, respectively, in cells treated for 48 h. Although both compounds interacted well with the active site, MD analysis suggests a second binding site with which BSB interacts via two hydrogen bonds, much more strongly than boldine. Theoretical analyses also evaluated the IC50 for BSB as submicromolar. BSB, with greater hydrophobicity and flexibility than boldine, represents a promising structure to inhibit telomerase at non-toxic concentrations.
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Affiliation(s)
- Sakineh Kazemi Noureini
- Department of Biology, Faculty of Sciences, Hakim Sabzevari University, Sabzevar 9617976487, Iran.
| | - Mitra Kheirabadi
- Department of Biology, Faculty of Sciences, Hakim Sabzevari University, Sabzevar 9617976487, Iran.
| | - Fatima Masoumi
- Department of Biology, Faculty of Sciences, Hakim Sabzevari University, Sabzevar 9617976487, Iran.
| | - Farve Khosrogerdi
- Department of Biology, Faculty of Sciences, Hakim Sabzevari University, Sabzevar 9617976487, Iran.
| | - Younes Zarei
- Department of Biology, Faculty of Sciences, Hakim Sabzevari University, Sabzevar 9617976487, Iran.
| | - Cristian Suárez-Rozas
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago 1058, Chile.
| | - Julio Salas-Norambuena
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago 1058, Chile.
| | - Bruce Kennedy Cassels
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago 1058, Chile.
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15
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Shastry S, Steinberg-Neifach O, Lue N, Stone MD. Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain. Nucleic Acids Res 2018; 46:3088-3102. [PMID: 29474579 PMCID: PMC5887506 DOI: 10.1093/nar/gky117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/31/2018] [Accepted: 02/17/2018] [Indexed: 11/12/2022] Open
Abstract
Telomerase is a specialized enzyme that maintains telomere length by adding DNA repeats to chromosome ends. The catalytic protein subunit of telomerase utilizes the integral telomerase RNA to direct telomere DNA synthesis. The telomerase essential N-terminal (TEN) domain is required for enzyme function; however, the precise mechanism of the TEN domain during catalysis is not known. We report a single-molecule study of dynamic TEN-induced conformational changes in its nucleic acid substrates. The TEN domain from the yeast Candida parapsilosis (Cp) exhibits a strong binding preference for double-stranded nucleic acids, with particularly high affinity for an RNA-DNA hybrid mimicking the template-product complex. Surprisingly, the telomere DNA repeat sequence from C. parapsilosis forms a DNA hairpin that also binds CpTEN with high affinity. Mutations to several residues in a putative nucleic acid-binding patch of CpTEN significantly reduced its affinity to the RNA-DNA hybrid and telomere DNA hairpin. Substitution of comparable residues in the related Candida albicans TEN domain caused telomere maintenance defects in vivo and decreased primer extension activity in vitro. Collectively, our results support a working model in which dynamic interactions with telomere DNA and the template-product hybrid underlie the functional requirement for the TEN domain during the telomerase catalytic cycle.
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Affiliation(s)
- Shankar Shastry
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Olga Steinberg-Neifach
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Neal Lue
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
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16
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Kurcinski M, Blaszczyk M, Ciemny MP, Kolinski A, Kmiecik S. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information. Biomed Eng Online 2017; 16:73. [PMID: 28830545 PMCID: PMC5568604 DOI: 10.1186/s12938-017-0363-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background The characterization of protein–peptide interactions is a challenge for computational molecular docking. Protein–peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models. Methods In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein–peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score. Results As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area. Conclusions The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein–peptide complexes guided by the knowledge of the binding interface.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Blaszczyk
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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17
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Hoffman H, Rice C, Skordalakes E. Structural Analysis Reveals the Deleterious Effects of Telomerase Mutations in Bone Marrow Failure Syndromes. J Biol Chem 2017; 292:4593-4601. [PMID: 28154186 DOI: 10.1074/jbc.m116.771204] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
Naturally occurring mutations in the ribonucleoprotein reverse transcriptase, telomerase, are associated with the bone marrow failure syndromes dyskeratosis congenita, aplastic anemia, and idiopathic pulmonary fibrosis. However, the mechanism by which these mutations impact telomerase function remains unknown. Here we present the structure of the human telomerase C-terminal extension (or thumb domain) determined by the method of single-wavelength anomalous diffraction to 2.31 Å resolution. We also used direct telomerase activity and nucleic acid binding assays to explain how naturally occurring mutations within this portion of telomerase contribute to human disease. The single mutations localize within three highly conserved regions of the telomerase thumb domain referred to as motifs E-I (thumb loop and helix), E-II, and E-III (the FVYL pocket, comprising the hydrophobic residues Phe-1012, Val-1025, Tyr-1089, and Leu-1092). Biochemical data show that the mutations associated with dyskeratosis congenita, aplastic anemia, and idiopathic pulmonary fibrosis disrupt the binding between the protein subunit reverse transcriptase of the telomerase and its nucleic acid substrates leading to loss of telomerase activity and processivity. Collectively our data show that although these mutations do not alter the overall stability or expression of telomerase reverse transcriptase, these rare genetic disorders are associated with an impaired telomerase holoenzyme that is unable to correctly assemble with its nucleic acid substrates, leading to incomplete telomere extension and telomere attrition, which are hallmarks of these diseases.
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Affiliation(s)
- Hunter Hoffman
- From the Department of Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania 19104 and
| | - Cory Rice
- From the Department of Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania 19104 and.,the Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Emmanuel Skordalakes
- From the Department of Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania 19104 and .,the Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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18
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Parks JW, Kappel K, Das R, Stone MD. Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. RNA (NEW YORK, N.Y.) 2017; 23:175-188. [PMID: 28096444 PMCID: PMC5238793 DOI: 10.1261/rna.058743.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein. FRET-guided modeling places the essential pseudoknot fold distal to the active site on a protein surface comprising the C-terminal element, a domain that shares structural homology with canonical polymerase thumb domains. An independently solved medium-resolution structure of Tetrahymena telomerase provides a blind test of our modeling methodology and sheds light on the structural homology of this domain across diverse organisms. Our smFRET-Rosetta models reveal nanometer-scale rearrangements within the RNA core domain during catalysis. Taken together, our FRET data and pseudoatomic molecular models permit us to propose a possible mechanism for how RNA core domain rearrangement is coupled to template hybrid elongation.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, California 94305, USA
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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19
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Toussi CA, Soheilifard R. A better prediction of conformational changes of proteins using minimally connected network models. Phys Biol 2017; 13:066013. [PMID: 28112101 DOI: 10.1088/1478-3975/13/6/066013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Elastic network models have recently been used for studying low-frequency collective motions of proteins. These models simplify the complexity that arises from normal mode analysis by considering a simplified potential involving a few parameters. Two common parameters in most of the elastic network models are cutoff radius and force constant. Although the latter has been studied extensively and even elaborate new models were introduced, for the former usually an ad-hoc cutoff radius is considered. Moreover, the quality of the network models is usually assessed by evaluating their prediction against experimental B-factors. In this work, we consider various common elastic network models with different cutoff radii and assess them by their ability to predict conformational changes of proteins in complexes from unbound to bound state. This prediction is performed by perturbing the unbound structure using a number of low-frequency normal modes of its network model to optimally fit the bound structure. We evaluated a dataset of 30 proteins with distinct unbound and bound structures using this criterion. The results showed that, opposed to the common calibration process based on B-factors, a meaningful relationship exists between the quality of the prediction and model parameters. It was shown that the cutoff radius has a major role in this prediction and minimally connected network models, which use the shortest cutoff radius for which the network is stable, give the best results. It was also shown that by considering the first ten normal modes, the conformational changes can be predicted by about 25 percent. Hence, the evaluation process was extended to the case of considering the contribution of all normal modes in the prediction. The results indicated that minimally connected network models are superior, despite their simplicity, when any number of modes are considered in the prediction.
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Affiliation(s)
- Cyrus Ahmadi Toussi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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20
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Kmiecik S, Kolinski A. One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model. Methods Mol Biol 2017; 1484:83-113. [PMID: 27787822 DOI: 10.1007/978-1-4939-6406-2_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps the most successful strategy to overcome the inefficiency problem is multiscale modeling to merge all-atom and coarse-grained models. This chapter describes a well-established CABS coarse-grained protein model. The CABS (C-Alpha, C-Beta, and Side chains) model assumes a 2-4 united-atom representation of amino acids, knowledge-based force field (derived from the statistical regularities seen in known protein sequences and structures) and efficient Monte Carlo sampling schemes (MC dynamics, MC replica-exchange, and combinations). A particular emphasis is given to the unique design of the CABS force-field, which is largely defined using one-dimensional structural properties of proteins, including protein secondary structure. This chapter also presents CABS-based modeling methods, including multiscale tools for de novo structure prediction, modeling of protein dynamics and prediction of protein-peptide complexes. CABS-based tools are freely available at http://biocomp.chem.uw.edu.pl/tools.
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Affiliation(s)
- Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warszawa, 02-093, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warszawa, 02-093, Poland.
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21
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Fuggetta MP, De Mico A, Cottarelli A, Morelli F, Zonfrillo M, Ulgheri F, Peluso P, Mannu A, Deligia F, Marchetti M, Roviello G, Reyes Romero A, Dömling A, Spanu P. Synthesis and Enantiomeric Separation of a Novel Spiroketal Derivative: A Potent Human Telomerase Inhibitor with High in Vitro Anticancer Activity. J Med Chem 2016; 59:9140-9149. [DOI: 10.1021/acs.jmedchem.6b01046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Pia Fuggetta
- Istituto di Farmacologia Traslazionale, Consiglio Nazionale delle
Ricerche, Via Fosso del Cavaliere, 00133 Roma, Italy
| | - Antonella De Mico
- Istituto
di Biologia e Patologia Molecolare, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Andrea Cottarelli
- Istituto di Farmacologia Traslazionale, Consiglio Nazionale delle
Ricerche, Via Fosso del Cavaliere, 00133 Roma, Italy
| | - Franco Morelli
- Istituto di Genetica
e Biofisica, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Manuela Zonfrillo
- Istituto di Farmacologia Traslazionale, Consiglio Nazionale delle
Ricerche, Via Fosso del Cavaliere, 00133 Roma, Italy
| | - Fausta Ulgheri
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
| | - Paola Peluso
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
| | - Alberto Mannu
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
| | - Francesco Deligia
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
| | - Mauro Marchetti
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
| | - Giovanni Roviello
- Istituto di Biostrutture e Bioimmagini,
Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Naples, Italy
| | - Atilio Reyes Romero
- Department of Drug Design,
School of Pharmacy, University of Groningen, Antonius Deusinglaan 1 Postbus 196, 9700 AD, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design,
School of Pharmacy, University of Groningen, Antonius Deusinglaan 1 Postbus 196, 9700 AD, Groningen, The Netherlands
| | - Pietro Spanu
- Istituto di Chimica Biomolecolare,
Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, 07100 Sassari, Italy
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22
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MacNeil DE, Bensoussan HJ, Autexier C. Telomerase Regulation from Beginning to the End. Genes (Basel) 2016; 7:genes7090064. [PMID: 27649246 PMCID: PMC5042394 DOI: 10.3390/genes7090064] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
The vast body of literature regarding human telomere maintenance is a true testament to the importance of understanding telomere regulation in both normal and diseased states. In this review, our goal was simple: tell the telomerase story from the biogenesis of its parts to its maturity as a complex and function at its site of action, emphasizing new developments and how they contribute to the foundational knowledge of telomerase and telomere biology.
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Affiliation(s)
- Deanna Elise MacNeil
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Hélène Jeanne Bensoussan
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Chantal Autexier
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
- Department of Experimental Medicine, McGill University, 1110 Pins Avenue West, Room 101, Montréal, QC H3A 1A3, Canada.
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23
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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24
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Identification of human telomerase inhibitors having the core of N -acyl-4,5-dihydropyrazole with anticancer effects. Bioorg Med Chem Lett 2016; 26:1508-1511. [DOI: 10.1016/j.bmcl.2016.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/28/2016] [Accepted: 02/10/2016] [Indexed: 02/01/2023]
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25
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Novel dihydropyrazole-chromen: Design and modulates hTERT inhibition proliferation of MGC-803. Eur J Med Chem 2016; 110:65-75. [DOI: 10.1016/j.ejmech.2016.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/10/2016] [Accepted: 01/11/2016] [Indexed: 01/22/2023]
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26
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Abstract
Fluorescence microscopy can be used to assess the dynamic localization and intensity of single entities
in vitro or in living cells. It has been applied with aplomb to many different cellular processes and has significantly enlightened our understanding of the heterogeneity and complexity of biological systems. Recently, high-resolution fluorescence microscopy has been brought to bear on telomeres, leading to new insights into telomere spatial organization and accessibility, and into the mechanistic nuances of telomere elongation. We provide a snapshot of some of these recent advances with a focus on mammalian systems, and show how three-dimensional, time-lapse microscopy and single-molecule fluorescence shine a new light on the end of the chromosome.
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Affiliation(s)
- Yahya Benslimane
- Department of Molecular Biology, University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Lea Harrington
- Department of Molecular Biology, University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada; Department of Biochemistry, University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada; Department of Medicine, University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
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27
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Wang Y, Cheng FX, Yuan XL, Tang WJ, Shi JB, Liao CZ, Liu XH. Dihydropyrazole derivatives as telomerase inhibitors: Structure-based design, synthesis, SAR and anticancer evaluation in vitro and in vivo. Eur J Med Chem 2016; 112:231-251. [PMID: 26900656 DOI: 10.1016/j.ejmech.2016.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 11/27/2022]
Abstract
It is of our interest to generate and identify novel compounds with regulation telomerase for cancer therapy. In order to carry out more rational design, based on structure-based drug design, several series of N-substituted-dihydropyrazole derivatives, totally 78 compounds as potential human telomerase inhibitors were designed and synthesized. The results demonstrated that some compounds had potent anticancer activity against four tumor cell lines, and showed good selectivity on tumor cells over somatic cells. By the modified TRAP assay, compound 13i exhibited the most potent inhibitory activity against telomerase with an IC50 value of 0.98 μM. In vivo evaluation results indicated that compound 13i could inhibit growth of S180 and HepG2 tumor-bearing mice, and it also significantly enhanced the survival rate of EAC tumor-bearing mice. The further results in vivo confirmed that it could significantly improve pathological changes of N,N-diethylnitrosamine (DEN)-induced rat hepatic tumor. These data support further studies to assess rational design of more efficient telomerase inhibitors in the future.
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Affiliation(s)
- Yang Wang
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China
| | - Fei Xiong Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Technology, Shanghai 200237, PR China
| | - Xiao Long Yuan
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Wen Jian Tang
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China
| | - Jing Bo Shi
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China
| | - Chen Zhong Liao
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China
| | - Xin Hua Liu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China.
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28
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Kurcinski M, Kolinski A, Kmiecik S. Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations. J Chem Theory Comput 2015; 10:2224-31. [PMID: 26580746 DOI: 10.1021/ct500287c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A complex of the phosphorylated kinase-inducible domain (pKID) with its interacting domain (KIX) is a model system for studies of mechanisms by which intrinsically unfolded proteins perform their functions. These mechanisms are not fully understood. Using an efficient coarse-grained model, ab initio simulations were performed of the coupled folding and binding of the pKID to the KIX. The simulations start from an unbound, randomly positioned and disordered pKID structure. During the simulations the pKID chain and its position remain completely unrestricted, while the KIX backbone is limited to near-native fluctuations. Ab initio simulations of such large-scale conformational transitions, unaffected by any knowledge about the bound pKID structure, remain inaccessible to classical simulations. Our simulations recover an ensemble of transient encounter complexes in good agreement with experimental results. We find that a key folding and binding step is linked to the formation of weak native interactions between a preformed nativelike fragment of a pKID helix and KIX surface. Once that nucleus forms, the pKID chain may condense from a largely disordered encounter ensemble to a natively bound and ordered conformation. The observed mechanism is reminiscent of a nucleation-condensation model, a common scenario for folding of globular proteins.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
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Shirgahi Talari F, Bagherzadeh K, Golestanian S, Jarstfer M, Amanlou M. Potent Human Telomerase Inhibitors: Molecular Dynamic Simulations, Multiple Pharmacophore-Based Virtual Screening, and Biochemical Assays. J Chem Inf Model 2015; 55:2596-610. [PMID: 26529120 DOI: 10.1021/acs.jcim.5b00336] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Telomere maintenance is a universal cancer hallmark, and small molecules that disrupt telomere maintenance generally have anticancer properties. Since the vast majority of cancer cells utilize telomerase activity for telomere maintenance, the enzyme has been considered as an anticancer drug target. Recently, rational design of telomerase inhibitors was made possible by the determination of high resolution structures of the catalytic telomerase subunit from a beetle and subsequent molecular modeling of the human telomerase complex. A hybrid strategy including docking, pharmacophore-based virtual screening, and molecular dynamics simulations (MDS) were used to identify new human telomerase inhibitors. Docking methodology was applied to investigate the ssDNA telomeric sequence and two well-known human telomerase inhibitors' (BIBR1532 and MST-312) modes of interactions with hTERT TEN domain. Subsequently molecular dynamic simulations were performed to monitor and compare hTERT TEN domain, TEN-ssDNA, TEN-BIBR1532, TEN-MST-312, and TEN-ssDNA-BIBR1532 behavior in a dynamic environment. Pharmacophore models were generated considering the inhibitors manner in the TEN domain anchor site. These exploratory studies identified several new potent inhibitors whose IC50 values were generated experimentally in a low micromolar range with the aid of biochemical assays, including both the direct telomerase and the telomeric repeat amplification protocol (TRAP) assays. The results suggest that the current models of human telomerase are useful templates for rational inhibitor design.
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Affiliation(s)
- Faezeh Shirgahi Talari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences , Tehran, 14155-6451, Iran.,Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Kowsar Bagherzadeh
- Razi Drug Research Center, Iran University of Medical Sciences , Tehran, 1449614535, Iran
| | - Sahand Golestanian
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences , Tehran, 14155-6451, Iran
| | - Michael Jarstfer
- Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences , Tehran, 14155-6451, Iran
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30
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Bryan C, Rice C, Hoffman H, Harkisheimer M, Sweeney M, Skordalakes E. Structural Basis of Telomerase Inhibition by the Highly Specific BIBR1532. Structure 2015; 23:1934-1942. [PMID: 26365799 DOI: 10.1016/j.str.2015.08.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 01/03/2023]
Abstract
BIBR1532 is a highly specific telomerase inhibitor, although the molecular basis for inhibition is unknown. Here we present the crystal structure of BIBR1532 bound to Tribolium castaneum catalytic subunit of telomerase (tcTERT). BIBR1532 binds to a conserved hydrophobic pocket (FVYL motif) on the outer surface of the thumb domain. The FVYL motif is near TRBD residues that bind the activation domain (CR4/5) of hTER. RNA binding assays show that the human TERT (hTERT) thumb domain binds the P6.1 stem loop of CR4/5 in vitro. hTERT mutations of the FVYL pocket alter wild-type CR4/5 binding and cause telomere attrition in cells. Furthermore, the hTERT FVYL mutations V1025F, N1028H, and V1090M are implicated in dyskeratosis congenita and aplastic anemia, further supporting the biological and clinical relevance of this novel motif. We propose that CR4/5 contacts with the telomerase thumb domain contribute to telomerase ribonucleoprotein assembly and promote enzymatic activity.
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Affiliation(s)
- Christopher Bryan
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Cory Rice
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hunter Hoffman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | - Melanie Sweeney
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Emmanuel Skordalakes
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA; Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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31
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Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 2015; 93:72-83. [PMID: 26165956 DOI: 10.1016/j.ymeth.2015.07.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.
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32
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Mozolewska MA, Krupa P, Scheraga HA, Liwo A. Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches. Proteins 2015; 83:1414-26. [PMID: 25973573 DOI: 10.1002/prot.24824] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/18/2015] [Accepted: 04/29/2015] [Indexed: 11/06/2022]
Abstract
The iron-sulfur protein 1 (Isu1) and the J-type co-chaperone Jac1 from yeast are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ-shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105 , L109 , and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1-12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N(95), T(98), P(102), H(112), V(159), L(167), and A(170) of Jac1, not yet tested experimentally, were also found to be important in binding.
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Affiliation(s)
- Magdalena A Mozolewska
- Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853-1301
| | - Paweł Krupa
- Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853-1301
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853-1301
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
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33
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Xue W, Song BA, Zhao HJ, Qi XB, Huang YJ, Liu XH. Novel myricetin derivatives: Design, synthesis and anticancer activity. Eur J Med Chem 2015; 97:155-63. [PMID: 25965778 DOI: 10.1016/j.ejmech.2015.04.063] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
Telomere and telomerase were closely related to occurrence and development of some cancers. To enhance ability of myricetin moiety for inhibiting telomerase, we designed a series of novel myricetin derivatives based on reasonable analysis. The telomerase inhibition assay showed that compound 6d displayed the most potent inhibitory activity with IC50 value of 0.91 μM. The anticancer activity assay showed that 6d exhibited high activity against human breast cells MDA-MB-231. The docking simulation of compound 6d was performed to get the probable binding model, the results demonstrated that the furan ring inserted into the active site deeply and had hydrophobic interactions with residues of Phe 568, Pro 627, four methoxy groups had hydrophobic interactions with residues of Phe 568, Pro 627, Lys 902, Val 904 and Pro 929. Western blot results showed that expression of p65 and TERT protein was clearly down-regulated by compound 6d. These data support further studies for the rational design of more efficient p65 and TERT modulators.
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Affiliation(s)
- Wei Xue
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 55002, PR China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 55002, PR China.
| | - Hong Ju Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 55002, PR China
| | - Xing Bao Qi
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China
| | - Yin Jiu Huang
- Department of Bioscience, Bengbu Medical College, Bengbu, 233030, PR China
| | - Xin Hua Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 55002, PR China; School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China.
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34
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Design and synthesis of celastrol derivatives as anticancer agents. Eur J Med Chem 2015; 95:166-73. [PMID: 25812966 DOI: 10.1016/j.ejmech.2015.03.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 01/18/2023]
Abstract
A series of celastrol derivatives as potential telomerase inhibitors were designed and synthesized. The bioassays demonstrated that title compounds displayed potent anticancer activities against SGC-7901, SMMC-7721, MGC-803 and HepG-2 cell lines, among them, compounds 3c and 3d which containing hydrophilicity moieties exhibited high anti-proliferative activities (IC50 = 0.10-1.22 μM). The preliminary mechanism of antitumor action indicated that title compound 3c could induce significant SMMC-7721 cells apoptosis. A modified TRAP assay showed that compounds 3c and 3d displayed the most potent inhibitory activity with IC50 values at 0.11 and 0.34 μM, respectively. And there was a good correlation between telomerase inhibition and anti-proliferative inhibition of SMMC-7721 cells. Moreover, molecular docking indicated that the active compound 3c was nicely bound into the telomerase hTERT active site, hydrophobic, van der Waals and two hydrogen bond interactions with conserved residues ASP 628 and TYR 949 were found.
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35
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Kmiecik S, Jamroz M, Kolinski M. Structure prediction of the second extracellular loop in G-protein-coupled receptors. Biophys J 2015; 106:2408-16. [PMID: 24896119 PMCID: PMC4052351 DOI: 10.1016/j.bpj.2014.04.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/26/2014] [Accepted: 04/17/2014] [Indexed: 12/29/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs.
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Affiliation(s)
- Sebastian Kmiecik
- University of Warsaw, Faculty of Chemistry, Laboratory of Theory of Biopolymers, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Jamroz
- University of Warsaw, Faculty of Chemistry, Laboratory of Theory of Biopolymers, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Mossakowski Medical Research Center, Polish Academy of Sciences, Bioinformatics Laboratory, Pawinskiego 5, 02-106 Warsaw, Poland.
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36
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Progress in structural studies of telomerase. Curr Opin Struct Biol 2014; 24:115-24. [PMID: 24508601 DOI: 10.1016/j.sbi.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/01/2014] [Accepted: 01/08/2014] [Indexed: 02/01/2023]
Abstract
Telomerase is the ribonucleoprotein (RNP) reverse transcriptase responsible for synthesizing the 3' ends of linear chromosomes. It plays critical roles in tumorigenesis, cellular aging, and stem cell renewal. The past two years have seen exciting progress in determining telomerase holoenzyme architecture and the structural basis of telomerase activity. Notably, the first electron microscopy structures of telomerase were reported, of the Tetrahymena thermophila telomerase holoenzyme and a human telomerase dimer. In addition to new structures of TERT and TER domains, the first structures of telomerase protein domains beyond TERT, and their complexes with TER or telomeric single-stranded DNA, were reported. Together these studies provide the first glimpse into the organization of the proteins and RNA in the telomerase RNP.
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37
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Sekaran V, Soares J, Jarstfer MB. Telomere Maintenance as a Target for Drug Discovery. J Med Chem 2013; 57:521-38. [DOI: 10.1021/jm400528t] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vijay Sekaran
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joana Soares
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael B. Jarstfer
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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38
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Jiang J, Miracco EJ, Hong K, Eckert B, Chan H, Cash DD, Min B, Zhou ZH, Collins K, Feigon J. The architecture of Tetrahymena telomerase holoenzyme. Nature 2013; 496:187-92. [PMID: 23552895 PMCID: PMC3817743 DOI: 10.1038/nature12062] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/08/2013] [Indexed: 01/15/2023]
Abstract
Telomerase adds telomeric repeats to chromosome ends using an internal RNA template and a specialized telomerase reverse transcriptase (TERT), thereby maintaining genome integrity. Little is known about the physical relationships among protein and RNA subunits within a biologically functional holoenzyme. Here we describe the architecture of Tetrahymena thermophila telomerase holoenzyme determined by electron microscopy. Six of the seven proteins and the TERT-binding regions of telomerase RNA (TER) have been localized by affinity labelling. Fitting with high-resolution structures reveals the organization of TERT, TER and p65 in the ribonucleoprotein (RNP) catalytic core. p50 has an unanticipated role as a hub between the RNP catalytic core, p75-p19-p45 subcomplex, and the DNA-binding Teb1. A complete in vitro holoenzyme reconstitution assigns function to these interactions in processive telomeric repeat synthesis. These studies provide the first view of the extensive network of subunit associations necessary for telomerase holoenzyme assembly and physiological function.
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Affiliation(s)
- Jiansen Jiang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
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39
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Park JK, Jernigan R, Wu Z. Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations. Bull Math Biol 2013; 75:124-60. [PMID: 23296997 DOI: 10.1007/s11538-012-9797-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 11/08/2012] [Indexed: 11/26/2022]
Abstract
We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C(α), C, N, and C(β) are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and their correlations with the experimental B-factors are calculated for a large set of proteins. The results are compared with all-atom normal mode analysis and the residue-level Gaussian Network Model. The coarse-grained methods perform more efficiently than all-atom normal mode analysis, while their B-factor correlations are also higher. Their B-factor correlations are comparable with those estimated by the Gaussian Network Model and in many cases better. The extracted force constants are surveyed for different pairs of residues with different numbers of separation residues in sequence. The statistical averages are used to build a refined Gaussian Network Model, which is able to predict residue-level structural fluctuations significantly better than the conventional Gaussian Network Model in many test cases.
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Affiliation(s)
- Jun-Koo Park
- Department of Mathematics, Iowa State University, Ames, IA 50010, USA.
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40
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Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. Elastic network normal modes provide a basis for protein structure refinement. J Chem Phys 2012; 136:195101. [PMID: 22612113 DOI: 10.1063/1.4710986] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
It is well recognized that thermal motions of atoms in the protein native state, the fluctuations about the minimum of the global free energy, are well reproduced by the simple elastic network models (ENMs) such as the anisotropic network model (ANM). Elastic network models represent protein dynamics as vibrations of a network of nodes (usually represented by positions of the heavy atoms or by the C(α) atoms only for coarse-grained representations) in which the spatially close nodes are connected by harmonic springs. These models provide a reliable representation of the fluctuational dynamics of proteins and RNA, and explain various conformational changes in protein structures including those important for ligand binding. In the present paper, we study the problem of protein structure refinement by analyzing thermal motions of proteins in non-native states. We represent the conformational space close to the native state by a set of decoys generated by the I-TASSER protein structure prediction server utilizing template-free modeling. The protein substates are selected by hierarchical structure clustering. The main finding is that thermal motions for some substates, overlap significantly with the deformations necessary to reach the native state. Additionally, more mobile residues yield higher overlaps with the required deformations than do the less mobile ones. These findings suggest that structural refinement of poorly resolved protein models can be significantly enhanced by reduction of the conformational space to the motions imposed by the dominant normal modes.
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Affiliation(s)
- Pawel Gniewek
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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41
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Hengesbach M, Akiyama BM, Stone MD. Single-molecule analysis of telomerase structure and function. Curr Opin Chem Biol 2011; 15:845-52. [PMID: 22057212 DOI: 10.1016/j.cbpa.2011.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/05/2011] [Accepted: 10/17/2011] [Indexed: 02/06/2023]
Abstract
The telomerase ribonucleoprotein is a specialized reverse transcriptase required to maintain protective chromosome end-capping structures called telomeres. In most cells, telomerase is not active and the natural shortening of telomeres with each round of DNA replication ultimately triggers cell growth arrest. In contrast, the presence of telomerase confers a high level of renewal capacity upon rapidly dividing cells. Telomerase is aberrantly activated in 90% of human cancers and thus represents an important target for anticancer therapeutics. However, the naturally low abundance of telomerase has hampered efforts to obtain high-resolution models for telomerase structure and function. To circumvent these challenges, single-molecule techniques have recently been employed to investigate telomerase assembly, structure, and catalysis.
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Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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42
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Sealey DCF, Kostic AD, LeBel C, Pryde F, Harrington L. The TPR-containing domain within Est1 homologs exhibits species-specific roles in telomerase interaction and telomere length homeostasis. BMC Mol Biol 2011; 12:45. [PMID: 22011238 PMCID: PMC3215184 DOI: 10.1186/1471-2199-12-45] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 10/18/2011] [Indexed: 12/03/2022] Open
Abstract
Background The first telomerase-associated protein (Est1) was isolated in yeast due to its essential role in telomere maintenance. The human counterparts EST1A, EST1B, and EST1C perform diverse functions in nonsense-mediated mRNA decay (NMD), telomere length homeostasis, and telomere transcription. Although Est1 and EST1A/B interact with the catalytic subunit of yeast and human telomerase (Est2 and TERT, respectively), the molecular determinants of these interactions have not been elaborated fully. Results To investigate the functional conservation of the EST1 protein family, we performed protein-protein interaction mapping and structure-function analysis. The domain in hEST1A most conserved between species, containing a TPR (tricotetrapeptide repeat), was sufficient for interaction of hEST1A with multiple fragments of hTERT including the N-terminus. Two mutations within the hTERT N-terminus that perturb in vivo function (NAAIRS92, NAAIRS122) did not affect this protein interaction. ScEst1 hybrids containing the TPR of hEST1A, hEST1B, or hEST1C were expressed in yeast strains lacking EST1, yet they failed to complement senescence. Point mutations within and outside the cognate ScEst1 TPR, chosen to disrupt a putative protein interaction surface, resulted in telomere lengthening or shortening without affecting recruitment to telomeres. Conclusions These results identify a domain encompassing the TPR of hEST1A as an hTERT interaction module. The TPR of S. cerevisiae Est1 is required for telomerase-mediated telomere length maintenance in a manner that appears separable from telomere recruitment. Discrete residues in or adjacent to the TPR of Est1 also regulate telomere length homeostasis.
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Affiliation(s)
- David C F Sealey
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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