1
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Grieco A, Ruiz-Fresneda MA, Gómez-Mulas A, Pacheco-García JL, Quereda-Moraleda I, Pey AL, Martin-Garcia JM. Structural dynamics at the active site of the cancer-associated flavoenzyme NQO1 probed by chemical modification with PMSF. FEBS Lett 2023; 597:2687-2698. [PMID: 37726177 DOI: 10.1002/1873-3468.14738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/02/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
A large conformational heterogeneity of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with various human diseases, has been observed to occur in the catalytic site of the enzyme. Here, we report the X-ray structure of NQO1 with phenylmethylsulfonyl fluoride (PMSF) at 1.6 Å resolution. Activity assays confirmed that, despite being covalently bound to the Tyr128 residue at the catalytic site, PMSF did not abolish NQO1 activity. This may indicate that the PMSF molecule does not reduce the high flexibility of Tyr128, thus allowing NADH and DCPIP substrates to bind to the enzyme. Our results show that targeting Tyr128, a key residue in NQO1 function, with small covalently bound molecules could possibly not be a good drug discovery strategy to inhibit this enzyme.
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Affiliation(s)
- Alice Grieco
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | | | | | | | - Isabel Quereda-Moraleda
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Physical Chemistry, Unit of Excellence in Applied Chemistry to Biomedicine and Environment, and Institute of Biotechnology, University of Granada, Granada, Spain
| | - Jose M Martin-Garcia
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
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2
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Shreevatsa B, Dharmashekara C, Swamy VH, Gowda MV, Achar RR, Kameshwar VH, Thimmulappa RK, Syed A, Elgorban AM, Al-Rejaie SS, Ortega-Castro J, Frau J, Flores-Holguín N, Shivamallu C, Kollur SP, Glossman-Mitnik D. Virtual Screening for Potential Phytobioactives as Therapeutic Leads to Inhibit NQO1 for Selective Anticancer Therapy. Molecules 2021; 26:molecules26226863. [PMID: 34833955 PMCID: PMC8622762 DOI: 10.3390/molecules26226863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
NAD(P)H:quinone acceptor oxidoreductase-1 (NQO1) is a ubiquitous flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory two-electron reductions of quinones, quinonimines, nitroaromatics, and azo dyes. NQO1 is a multifunctional antioxidant enzyme whose expression and deletion are linked to reduced and increased oxidative stress susceptibilities. NQO1 acts as both a tumor suppressor and tumor promoter; thus, the inhibition of NQO1 results in less tumor burden. In addition, the high expression of NQO1 is associated with a shorter survival time of cancer patients. Inhibiting NQO1 also enables certain anticancer agents to evade the detoxification process. In this study, a series of phytobioactives were screened based on their chemical classes such as coumarins, flavonoids, and triterpenoids for their action on NQO1. The in silico evaluations were conducted using PyRx virtual screening tools, where the flavone compound, Orientin showed a better binding affinity score of −8.18 when compared with standard inhibitor Dicumarol with favorable ADME properties. An MD simulation study found that the Orientin binding to NQO1 away from the substrate-binding site induces a potential conformational change in the substrate-binding site, thereby inhibiting substrate accessibility towards the FAD-binding domain. Furthermore, with this computational approach we are offering a scope for validation of the new therapeutic components for their in vitro and in vivo efficacy against NQO1.
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Affiliation(s)
- Bhargav Shreevatsa
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Chandan Dharmashekara
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Vikas Halasumane Swamy
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Meghana V. Gowda
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Vivek Hamse Kameshwar
- School of Natural Science, Adichunchanagiri University, B.G. Nagara, Nagamangala, Mandya 571448, India;
| | - Rajesh Kumar Thimmulappa
- Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India;
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia;
| | - Joaquín Ortega-Castro
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Shiva Prasad Kollur
- Department of Sciences, Mysuru Campus, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru 570026, India
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
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3
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Godoy-Castillo C, Bravo-Acuña N, Arriagada G, Faunes F, León R, Soto-Delgado J. Identification of the naphthoquinone derivative inhibitors binding site in heat shock protein 90: an induced-fit docking, molecular dynamics and 3D-QSAR study. J Biomol Struct Dyn 2020; 39:5977-5987. [PMID: 32799638 DOI: 10.1080/07391102.2020.1803134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The combination of molecular modeling methods to identify the putative binding site of inhibitors constitutes an important tool in drug discovery. In this work, we used these analyses to understand the potent inhibitory effect of naphthoquinone derivatives on heat shock protein 90 (Hsp90), one of the proteins involved in many types of cancer. Molecular docking results indicated that some favorable interactions of key amino acid residues at the binding site of Hsp90 with these quinones would be responsible for the inhibition of Hsp90 activity. Molecular docking and molecular dynamics simulation were carried out to further understand the binding modes and the interactions between the protein and these inhibitors. The main residues of the internal cavity were Val136, Phe138, Tyr139, Val150, Trp162 and Val186. The high concordance between the docking results and 3D-QSAR contour maps gives us helpful information about the environment of the binding site. Our results provide the bases for a rational modification of new molecules based in quinone scaffold, in order to design more potent Hsp90 inhibitors, which would exhibit highly potent antitumor activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Claudio Godoy-Castillo
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Viña del Mar, Chile
| | - Nicolas Bravo-Acuña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Viña del Mar, Chile
| | - Gloria Arriagada
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la vida, Universidad Andrés Bello, Santiago, Chile
| | - Fernando Faunes
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
| | - Roberto León
- Departamento de Ciencias de la Ingeniería, Facultad de Ingeniería, Universidad Andrés Bello, Viña del Mar, Chile
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Viña del Mar, Chile
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4
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Zhang L, Liu Q, Huang L, Yang F, Liu A, Zhang J. Combination of lapatinib and luteolin enhances the therapeutic efficacy of lapatinib on human breast cancer through the FOXO3a/NQO1 pathway. Biochem Biophys Res Commun 2020; 531:364-371. [PMID: 32800546 DOI: 10.1016/j.bbrc.2020.07.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Breast cancer is a malignant disease and a great cause of morbidity and mortality in women. The etiology of breast cancer is complex and closely related to people's living habits. Lapatinib, a tyrosine-kinase inhibitor, blocks the activation of the HER1 and HER2 tyrosine kinase to inhibit the activation of downstream signaling pathways and thus inhibit tumor survival and proliferation. This study aimed to explore to the combination of lapatinib and luteolin on human breast cancer. The combination of lapatinib and luteolin increased the sensitivity of SKBR-3, BT-474 and ZR-75-1 cells. This combination equally up-regulated the expression of FOXO3a and NQO1 and their downstream target genes Bim, GADD45, P21, and the phosphorylation level of FOXO3a protein decreased. The mice transplanted with BT-474 cells, the volume of subcutaneous tumors in the luteolin group, lapatinib group, and lapatinib + luteolin group were significantly smaller than the control group. The results of Western blot showed that in tumor tissues of mice transplanted with BT-474 cells, the expression levels of FOXO3a and NQO1 protein in the luteolin group, lapatinib group, and lapatinib + luteolin group were all obviously upregulated, the mice transplanted with ZR-75-1 cells exhibited similar results. These data suggest that the combination of lapatinib and luteolin may inhibit HER2+ human breast cancer by significantly increasing the expression of FOXO3a and NQO1, two key genes in HER2+ human breast cancer xenografts.
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Affiliation(s)
- Lingyan Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China; Department of Health Management, Chongqing Bishan District People's Hospital, Chongqing, 402760, China
| | - Qingjun Liu
- Department of E.N.T, Chongqing Bishan District People's Hospital, Chongqing, 402760, China
| | - Li Huang
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Fan Yang
- Department of Oncology, Xiangtan First People's Hospital, Xiangtan, 411101, China
| | - Aixue Liu
- Department of Oncology, Shenzhen Second People's Hospital, Shenzhen, 518000, China
| | - Jiren Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
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5
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Megarity CF, Abdel‐Aal Bettley H, Caraher MC, Scott KA, Whitehead RC, Jowitt TA, Gutierrez A, Bryce RA, Nolan KA, Stratford IJ, Timson DJ. Negative Cooperativity in NAD(P)H Quinone Oxidoreductase 1 (NQO1). Chembiochem 2019; 20:2841-2849. [DOI: 10.1002/cbic.201900313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Clare F. Megarity
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
| | - Hoda Abdel‐Aal Bettley
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - M. Clare Caraher
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Katherine A. Scott
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Roger C. Whitehead
- Department of ChemistryThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Thomas A. Jowitt
- The Faculty of Life ScienceManchester Cancer Research Centre and the University of Manchester Oxford Road Manchester M13 9PT UK
| | - Aldo Gutierrez
- School of Science and TechnologyNottingham Trent University Clifton Campus Nottingham NG11 8NS UK
| | - Richard A. Bryce
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Karen A. Nolan
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Ian J. Stratford
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - David J. Timson
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
- School of Pharmacy and Biomolecular Sciences, Huxley BuildingUniversity of Brighton Lewes Road Brighton BN2 4GJ UK
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6
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Beaver SK, Mesa-Torres N, Pey AL, Timson DJ. NQO1: A target for the treatment of cancer and neurological diseases, and a model to understand loss of function disease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:663-676. [PMID: 31091472 DOI: 10.1016/j.bbapap.2019.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
NAD(P)H quinone oxidoreductase 1 (NQO1) is a multi-functional protein that catalyses the reduction of quinones (and other molecules), thus playing roles in xenobiotic detoxification and redox balance, and also has roles in stabilising apoptosis regulators such as p53. The structure and enzymology of NQO1 is well-characterised, showing a substituted enzyme mechanism in which NAD(P)H binds first and reduces an FAD cofactor in the active site, assisted by a charge relay system involving Tyr-155 and His-161. Protein dynamics play important role in physio-pathological aspects of this protein. NQO1 is a good target to treat cancer due to its overexpression in cancer cells. A polymorphic form of NQO1 (p.P187S) is associated with increased cancer risk and certain neurological disorders (such as multiple sclerosis and Alzheimer´s disease), possibly due to its roles in the antioxidant defence. p.P187S has greatly reduced FAD affinity and stability, due to destabilization of the flavin binding site and the C-terminal domain, which leading to reduced activity and enhanced degradation. Suppressor mutations partially restore the activity of p.P187S by local stabilization of these regions, and showing long-range allosteric communication within the protein. Consequently, the correction of NQO1 misfolding by pharmacological chaperones is a viable strategy, which may be useful to treat cancer and some neurological conditions, targeting structural spots linked to specific disease-mechanisms. Thus, NQO1 emerges as a good model to investigate loss of function mechanisms in genetic diseases as well as to improve strategies to discriminate between neutral and pathogenic variants in genome-wide sequencing studies.
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Affiliation(s)
- Sarah K Beaver
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain
| | - Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain.
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
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7
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Selvakumar R, Anantha Krishnan D, Ramakrishnan C, Velmurugan D, Gunasekaran K. Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches. J Biomol Struct Dyn 2019; 38:682-696. [DOI: 10.1080/07391102.2019.1585291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rajendran Selvakumar
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | | | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - Devadasan Velmurugan
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Krishnasamy Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Chennai, Tamil Nadu, India
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NAD(P)H quinone oxidoreductase (NQO1): an enzyme which needs just enough mobility, in just the right places. Biosci Rep 2019; 39:BSR20180459. [PMID: 30518535 PMCID: PMC6328894 DOI: 10.1042/bsr20180459] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/23/2022] Open
Abstract
NAD(P)H quinone oxidoreductase 1 (NQO1) catalyses the two electron reduction of quinones and a wide range of other organic compounds. Its physiological role is believed to be partly the reduction of free radical load in cells and the detoxification of xenobiotics. It also has non-enzymatic functions stabilising a number of cellular regulators including p53. Functionally, NQO1 is a homodimer with two active sites formed from residues from both polypeptide chains. Catalysis proceeds via a substituted enzyme mechanism involving a tightly bound FAD cofactor. Dicoumarol and some structurally related compounds act as competitive inhibitors of NQO1. There is some evidence for negative cooperativity in quinine oxidoreductases which is most likely to be mediated at least in part by alterations to the mobility of the protein. Human NQO1 is implicated in cancer. It is often over-expressed in cancer cells and as such is considered as a possible drug target. Interestingly, a common polymorphic form of human NQO1, p.P187S, is associated with an increased risk of several forms of cancer. This variant has much lower activity than the wild-type, primarily due to its substantially reduced affinity for FAD which results from lower stability. This lower stability results from inappropriate mobility of key parts of the protein. Thus, NQO1 relies on correct mobility for normal function, but inappropriate mobility results in dysfunction and may cause disease.
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