scholarly journals In Silico Drug Repurposing by Structural Alteration after Induced Fit: Discovery of a Candidate Agent for Recovery of Nucleotide Excision Repair in Xeroderma Pigmentosum Group D Mutant (R683W)

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 249
Author(s):  
Yutaka Takaoka ◽  
Mika Ohta ◽  
Satoshi Tateishi ◽  
Aki Sugano ◽  
Eiji Nakano ◽  
...  
Keyword(s):  
Nucleotide Excision Repair ◽  
In Silico ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Drug Repurposing ◽  
Complementation Group ◽  
Drug Candidate ◽  
Induced Fit ◽  
Nucleotide Excision ◽  
Group D

Xeroderma pigmentosum complementation group D (XPD) is a UV-sensitive syndrome and a rare incurable genetic disease which is caused by the genetic mutation of the excision repair cross-complementation group 2 gene (ERCC2). Patients who harbor only XPD R683W mutant protein develop severe photosensitivity and progressive neurological symptoms. Cultured cells derived from patients with XPD (XPD R683W cells) demonstrate a reduced nucleotide excision repair (NER) ability. We hope to ameliorate clinical symptoms if we can identify candidate agents that would aid recovery of the cells’ NER ability. To investigate such candidates, we created in silico methods of drug repurposing (in silico DR), a strategy that utilizes the recovery of ATP-binding in the XPD R683W protein after the induced fit. We chose 4E1RCat and aprepitant as the candidates for our in silico DR, and evaluated them by using the UV-induced unscheduled DNA synthesis (UDS) assay to verify the recovery of NER in XPD R683W cells. UDS values of the cells improved about 1.4–1.7 times after 4E1RCat treatment compared with solvent-only controls; aprepitant showed no positive effect. In this study, therefore, we succeeded in finding the candidate agent 4E1RCat for XPD R683W. We also demonstrated that our in silico DR method is a cost-effective approach for drug candidate discovery.

The XPD helicase: XPanDing archaeal XPD structures to get a grip on human DNA repair

2010 ◽  
Vol 391 (7) ◽  
Author(s):  
Stefanie C. Wolski ◽  
Jochen Kuper ◽  
Caroline Kisker
Keyword(s):  
Transcription Initiation ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Complementation Group ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Iron Sulfur ◽  
Nucleotide Excision ◽  
Xpd Helicase ◽  
Group D

Abstract Xeroderma pigmentosum complementation group D protein (XPD) is an iron-sulfur cluster containing 5′-3′ helicase and, in humans, part of the transcription factor TFIIH. TFIIH is involved in nucleotide excision repair as well as in transcription initiation. Recently, three different groups have reported the structures of archaeal XPDs. All structures revealed a four-domain organization with two RecA-like domains, an Arch domain and an iron-sulfur cluster domain. It was possible to rationalize several of the mutations in the human XPD gene that lead to one of the three severe diseases xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. The different structures are compared and disease-related mutations are discussed.

scholarly journals Xeroderma Pigmentosum Diagnosis Using a Flow Cytometry-Based Nucleotide Excision Repair Assay

2018 ◽  
Vol 138 (2) ◽  
pp. 467-470 ◽  
Author(s):  
Eiji Nakano ◽  
Seiji Takeuchi ◽  
Ryusuke Ono ◽  
Mariko Tsujimoto ◽  
Taro Masaki ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Nucleotide Excision Repair ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Nucleotide Excision

scholarly journals Nucleotide excision repair syndromes: molecular basis and clinical symptoms

1995 ◽  
Vol 347 (1319) ◽  
pp. 75-81 ◽  
Keyword(s):  
Nucleotide Excision Repair ◽  
Transcription Initiation ◽  
Clinical Symptoms ◽  
Excision Repair ◽  
Complementation Group ◽  
Molecular Defect ◽  
Cockayne's Syndrome ◽  
Nucleotide Excision ◽  
Group B ◽  
Deficiency Diseases

The phenotypic consequences of a nucleotide excision repair (NER) defect in man are apparent from three distinct inborn diseases characterized by hypersensitivity of the skin to ultraviolet light and a remarkable clinical and genetic heterogeneity. These are the prototype repair syndrome, xeroderma pigmentosum (XP) (seven genetic complementation groups, designated XP-A to XP-G), Cockayne’s syndrome (two groups: CS-A and CS-B) and PIBIDS, a peculiar photosensitive form of the brittle hair disease trichothiodystrophy (TTD, at least two groups of which one equivalent to XP-D). To investigate the mechanism of NER and to resolve the molecular defect in these NER deficiency diseases we have focused on the cloning and characterization of human DNA repair genes. One of the genes that we cloned is ERCC3 . It specifies a chromatin binding helicase. Transfection and microinjection experiments demonstrated that mutations in ERCC3 are responsible for XP complementation group B, a very rare form of XP that is simultaneously associated with Cockayne’s syndrome (CS). The ERCC3 protein was found to be part of a multiprotein complex (TFIIH) required for transcription initiation of most structural genes and for NER . This defines the additional, hitherto unknown vital function of the gene. This ERCC3 gene and several other ner genes involved in transcription initiation will be discussed.

scholarly journals The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair

2020 ◽  
Vol 48 (17) ◽  
pp. 9943-9958
Author(s):  
Rocío González-Corrochano ◽  
Federico M Ruiz ◽  
Nicholas M I Taylor ◽  
Sonia Huecas ◽  
Srdja Drakulic ◽  
...  
Keyword(s):  
Dna Binding ◽  
Xeroderma Pigmentosum ◽  
Mutational Analysis ◽  
Excision Repair ◽  
Genetic Diseases ◽  
Complementation Group ◽  
Repair System ◽  
High Plasticity ◽  
Starting Point ◽  
Nucleotide Excision

Abstract Nucleotide excision repair (NER) is an essential pathway to remove bulky lesions affecting one strand of DNA. Defects in components of this repair system are at the ground of genetic diseases such as xeroderma pigmentosum (XP) and Cockayne syndrome (CS). The XP complementation group G (XPG) endonuclease cleaves the damaged DNA strand on the 3′ side of the lesion coordinated with DNA re-synthesis. Here, we determined crystal structures of the XPG nuclease domain in the absence and presence of DNA. The overall fold exhibits similarities to other flap endonucleases but XPG harbors a dynamic helical arch that is uniquely oriented and defines a gateway. DNA binding through a helix-2-turn-helix motif, assisted by one flanking α-helix on each side, shows high plasticity, which is likely relevant for DNA scanning. A positively-charged canyon defined by the hydrophobic wedge and β-pin motifs provides an additional DNA-binding surface. Mutational analysis identifies helical arch residues that play critical roles in XPG function. A model for XPG participation in NER is proposed. Our structures and biochemical data represent a valuable tool to understand the atomic ground of XP and CS, and constitute a starting point for potential therapeutic applications.

Nucleotide Excision Repair in the Three Domains of Life

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
David A Farnell
Keyword(s):  
Dna Repair ◽  
Nucleotide Excision Repair ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Human Diseases ◽  
Repair Pathway ◽  
Functional Conservation ◽  
Wide Range ◽  
Nucleotide Excision ◽  
Domains Of Life

Nucleotide excision repair (NER) is a vital DNA repair pathway which acts on a wide range of helix-distorting lesions. The importance of this pathway is highlighted by its functional conservation throughout evolution and by several human diseases, such as xeroderma pigmentosum, which are caused by a defective NER pathway. This review summarizes the NER mechanisms present in all three domains of life: eukaryotes, bacteria, and archaea.

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