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Ramzan S, Tennstedt S, Tariq M, Khan S, Noor Ul Ayan H, Ali A, Munz M, Thiele H, Korejo AA, Mughal AR, Jamal SZ, Nürnberg P, Baig SM, Erdmann J, Ahmad I. A Novel Missense Mutation in TNNI3K Causes Recessively Inherited Cardiac Conduction Disease in a Consanguineous Pakistani Family. Genes (Basel) 2021; 12:genes12081282. [PMID: 34440456 PMCID: PMC8395014 DOI: 10.3390/genes12081282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Cardiac conduction disease (CCD), which causes altered electrical impulse propagation in the heart, is a life-threatening condition with high morbidity and mortality. It exhibits genetic and clinical heterogeneity with diverse pathomechanisms, but in most cases, it disrupts the synchronous activity of impulse-generating nodes and impulse-conduction underlying the normal heartbeat. In this study, we investigated a consanguineous Pakistani family comprised of four patients with CCD. We applied whole exome sequencing (WES) and co-segregation analysis, which identified a novel homozygous missense mutation (c.1531T>C;(p.Ser511Pro)) in the highly conserved kinase domain of the cardiac troponin I-interacting kinase (TNNI3K) encoding gene. The behaviors of mutant and native TNNI3K were compared by performing all-atom long-term molecular dynamics simulations, which revealed changes at the protein surface and in the hydrogen bond network. Furthermore, intra and intermolecular interaction analyses revealed that p.Ser511Pro causes structural variation in the ATP-binding pocket and the homodimer interface. These findings suggest p.Ser511Pro to be a pathogenic variant. Our study provides insights into how the variant perturbs the TNNI3K structure-function relationship, leading to a disease state. This is the first report of a recessive mutation in TNNI3K and the first mutation in this gene identified in the Pakistani population.
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Affiliation(s)
- Shafaq Ramzan
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
| | - Stephanie Tennstedt
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- DZHK (German Research Centre for Cardiovascular Research) Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- University Heart Center Lübeck, 23562 Lübeck, Germany
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
| | - Hafiza Noor Ul Ayan
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
| | - Matthias Munz
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- DZHK (German Research Centre for Cardiovascular Research) Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (H.T.); (P.N.)
| | - Asad Aslam Korejo
- National Institute of Cardiovascular Disease, Karachi 75510, Pakistan; (A.A.K.); (S.Z.J.)
| | | | - Syed Zahid Jamal
- National Institute of Cardiovascular Disease, Karachi 75510, Pakistan; (A.A.K.); (S.Z.J.)
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (H.T.); (P.N.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany
| | - Shahid Mahmood Baig
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan; (M.T.); (S.K.); (A.A.); (S.M.B.)
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
- Pakistan Science Foundation (PSF), 1-Constitution Avenue, G-5/2, Islamabad 44000, Pakistan
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- DZHK (German Research Centre for Cardiovascular Research) Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- University Heart Center Lübeck, 23562 Lübeck, Germany
| | - Ilyas Ahmad
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.R.); (S.T.); (H.N.U.A.); (M.M.); (J.E.)
- DZHK (German Research Centre for Cardiovascular Research) Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- University Heart Center Lübeck, 23562 Lübeck, Germany
- Correspondence: ; Tel.: +49-(0)451-3101-8320
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Balasubramanian PK, Balupuri A, Bhujbal SP, Cho SJ. 3D-QSAR Assisted Design of Novel 7-Deazapurine Derivatives as TNNI3K Kinase Inhibitors Using Molecular Docking and Molecular Dynamics Simulation. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190110121300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Cardiac troponin I-interacting kinase (TNNI3K) is a cardiac-specific kinase
that belongs to MAPKKK family. It is a dual-function kinase with tyrosine and serine/threonine
kinase activity. Over-expression of TNNI3K results in various cardiovascular diseases such as
cardiomyopathy, ischemia/reperfusion injury, heart failure, etc. Since, it is a cardiac-specific kinase
and expressed only in heart tissue, it is an ideal molecular target to treat cardiac diseases. The main
objective of the work is to study and understand the structure-activity relationship of the reported
deazapurine derivatives and to use the 3D-QSAR and docking results to design potent and novel
TNNI3K inhibitors of this series.
Methods:
In the present study, we have used molecular docking 3D QSAR, and molecular dynamics
simulation to understand the structure-activity correlation of reported TNNI3K inhibitors and to
design novel compounds of deazapurine derivatives with increased activity.
Results:
Both CoMFA (q2=0.669, NOC=5, r2=0.944) and CoMSIA (q2=0.783, NOC=5, r2=0.965)
have resulted in satisfactory models. The models were validated using external test set, Leave-out-
Five, bootstrapping, progressive scrambling, and rm2 metrics calculations. The validation procedures
showed the developed models were robust and reliable. The docking results and the contour maps
analysis helped in the better understanding of the structure-activity relationship.
Conclusion:
This is the first report on 3D-QSAR modeling studies of TNNI3K inhibitors. Both
docking and MD results were consistent and showed good correlation with the previous experimental
data. Based on the information obtained from contour maps, 31 novel TNNI3K inhibitors were
designed. These designed compounds showed higher activity than the existing dataset compounds.
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Affiliation(s)
| | - Anand Balupuri
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea
| | - Swapnil P. Bhujbal
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea
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Xi Y, Honeywell C, Zhang D, Schwartzentruber J, Beaulieu CL, Tetreault M, Hartley T, Marton J, Vidal SM, Majewski J, Aravind L, Gollob M, Boycott KM, Gow RM. Whole exome sequencing identifies the TNNI3K gene as a cause of familial conduction system disease and congenital junctional ectopic tachycardia. Int J Cardiol 2015; 185:114-6. [PMID: 25791106 DOI: 10.1016/j.ijcard.2015.03.130] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/07/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Yanwei Xi
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Christina Honeywell
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Chandree L Beaulieu
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Martine Tetreault
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Taila Hartley
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Jennifer Marton
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Michael Gollob
- Toronto General Hospital, Department of Cardiology, University of Toronto, Toronto, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada; Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.
| | - Robert M Gow
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.
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