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Rai GP, Shanker A. Coevolution-based computational approach to detect resistance mechanism of epidermal growth factor receptor. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119592. [PMID: 37730130 DOI: 10.1016/j.bbamcr.2023.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/24/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Tyrosine kinase epidermal growth factor receptor (EGFR) correlates the neoplastic cell metastasis, angiogenesis, neoplastic incursion, and apoptosis. Due to the involvement of EGFR in these biological processes, it becomes a most potent target for treating non-small cell lung cancer (NSCLC). The tyrosine kinase inhibitors (TKI) have endorsed high efficacy and anticipation to patients but unfortunately, within a year of treatment, drug targets develop resistance due to mutations. The present study detected the compensatory mutations in EGFR to know the evolutionary mechanism of drug resistance. The results of this study demonstrate that compensatory mutations enlarge the drug-binding pocket which may lead to the altered orientation of the ligand (gefitinib and erlotinib) causing drug resistance. This indicates that coevolutionary forces play a significant role in fine-tuning the structure of EGFR protein against the drugs. The analysis provides insight into the evolution-induced structural aspects of drug resistance changes in EGFR which in turn be useful in designing drugs with better efficacy.
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Affiliation(s)
- Gyan Prakash Rai
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar 824236, India
| | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar 824236, India.
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Chikhale V, Goswami N, Khan MA, Borah P, Varma AK. Evaluation of Pathogenicity and Structural Alterations for the Mutations Identified in the Conserved Region of the C-Terminal Kinase Domain of Human-Ribosomal S6 Kinase 1. ACS OMEGA 2023; 8:16273-16283. [PMID: 37179615 PMCID: PMC10173430 DOI: 10.1021/acsomega.3c00722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/23/2023] [Indexed: 05/15/2023]
Abstract
Human-ribosomal s6 kinase 1 (h-RSK1) is an effector kinase of the Ras/MAPK signaling pathway, which is involved in the regulation of the cell cycle, proliferation, and survival. RSKs comprise two functionally distinct kinase domains at the N-terminal (NTKD) and C-terminal (CTKD) separated by a linker region. The mutations in RSK1 may have the potential to provide an extra benefit to the cancer cell to proliferate, migrate, and survive. The present study focuses on evaluating the structural basis for the missense mutations identified at the C-terminal kinase domain of human-RSK1. A total of 139 mutations reported on RSK1 were retrieved from cBioPortal, where 62 were located at the CTKD region. Furthermore, 10 missense mutations Arg434Pro, Thr701Met, Ala704Thr, Arg725Trp, Arg726Gln, His533Asn, Pro613Leu, Ser720Cys, Arg725Gln, and Ser732Phe were predicted to be deleterious using in silico tools. To our observation, these mutations are located in the evolutionarily conserved region of RSK1 and shown to alter the inter- and intramolecular interactions and also the conformational stability of RSK1-CTKD. The molecular dynamics (MD) simulation study further revealed that the five mutations Arg434Pro, Thr701Met, Ala704Thr, Arg725Trp, and Arg726Gln showed maximum structural alterations in RSK1-CTKD. Thus, based on the in silico and MD simulation analysis, it can be concluded that the reported mutations may serve as potential candidates for further functional studies.
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Affiliation(s)
- Vaishnvee Chikhale
- Advanced
Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra 410210, India
- Training
School Complex, Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Nabajyoti Goswami
- Advanced
Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra 410210, India
| | - Mudassar Ali Khan
- Advanced
Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra 410210, India
- Training
School Complex, Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Probodh Borah
- Bioinformatics
Infrastructure Facility, Department of Animal Biotechnology, Assam Agricultural University, Khanapara, Guwahati, Assam 781022, India
| | - Ashok K. Varma
- Advanced
Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra 410210, India
- Training
School Complex, Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra 400094, India
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Zacchia M, Capolongo G, Del Vecchio Blanco F, Secondulfo F, Gupta N, Blasio G, Pollastro RM, Cervesato A, Piluso G, Gigliotti G, Torella A, Nigro V, Perna AF, Capasso G, Trepiccione F. Next-Generation Sequencing (NGS) Analysis Illustrates the Phenotypic Variability of Collagen Type IV Nephropathies. Genes (Basel) 2023; 14:genes14030764. [PMID: 36981034 PMCID: PMC10048128 DOI: 10.3390/genes14030764] [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: 01/24/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Mutations in COL4A3-A5 cause a spectrum of glomerular disorders, including thin basement membrane nephropathy (TBMN) and Alport syndrome (AS). The wide application of next-generation sequencing (NGS) in the last few years has revealed that mutations in these genes are not limited to these clinical entities. In this study, 176 individuals with a clinical diagnosis of inherited kidney disorders underwent an NGS-based analysis to address the underlying cause; those who changed or perfected the clinical diagnosis after molecular analysis were selected. In 5 out of 83 individuals reaching a molecular diagnosis, the genetic result was unexpected: three individuals showed mutations in collagen type IV genes. These patients showed the following clinical pictures: (1) familial focal segmental glomerulosclerosis; (2) end-stage renal disease (ESRD) diagnosed incidentally in a 49-year-old man, with diffuse cortical calcifications on renal imaging; and (3) dysmorphic and asymmetric kidneys with multiple cysts and signs of tubule-interstitial defects. Genetic analysis revealed rare heterozygote/compound heterozygote COL4A4-A5 variants. Our study highlights the key role of NGS in the diagnosis of inherited renal disorders and shows the phenotype variability in patients carrying mutations in collagen type IV genes.
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Affiliation(s)
- Miriam Zacchia
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Giovanna Capolongo
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | | | - Floriana Secondulfo
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Neha Gupta
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
- Biogem, Scarl, 83031 Ariano Irpino, Italy
| | - Giancarlo Blasio
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Rosa Maria Pollastro
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Angela Cervesato
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Giuseppe Gigliotti
- UOC Nefrologia e Dialisi, Ospedale Civile di Eboli "MM.SS. Addolorata", 84025 Eboli, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Alessandra F Perna
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
| | | | - Francesco Trepiccione
- Department of Medical and Translational Sciences, University of Campania, Luigi Vanvitelli, 81100 Caserta, Italy
- Biogem, Scarl, 83031 Ariano Irpino, Italy
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