Kronik Miyeloid Lösemi (KML) ile İlişkili ABL1 Genindeki Tek Nükleotid Varyasyonlarının (SNV'ler) ve Tirozin Kinaz İnhibitörlerinin (TKI'ler) Etkinliğinin Biyoinformatik Araçlarla Değerlendirilmesi

Öz

ABL1 proteini, kronik miyeloid lösemi (KML) patogenezinde kritik rol oynamaktadır. KML tedavisinde, ABL1’in ATP ve miristoil bağlanma ceplerini hedef alan tirozin kinaz inhibitörleri (TKI’ler) kullanılmaktadır. Bu çalışmada, ABL1 protein kinaz domainindeki missense varyasyonların protein stabilitesi ve TKI bağlanma afiniteleri üzerindeki etkilerini değerlendirmek amaçlanmıştır. ABL1 protein kinaz domaininde yer alan 201 missense varyasyonu incelenmiş, ATP ve miristoil bağlanma bölgelerini etkileyebilecek toplam 224 aminoasit değişimi analiz edilmiştir. Protein stabilitesine etkiler MAESTRO-web, I-Mutant 2.0, DUET, SDM, CUPSAT ve MUpro ile tahmin edilmiştir. Tüm araçlarda destabilize edici bulunan varyasyonlar Swiss-Model DeepView ile modellenmiş, yabanıl tip ABL1 referans alınarak AutoDock Vina ile Imatinib, Dasatinib, Nilotinib, Bosutinib, Ponatinib ve Asciminib bağlanma afiniteleri hesaplanmıştır. Fonksiyonel etkiler PolyPhen2, PHD-SNP, PredictProtein ve PANTHER ile belirlenmiştir. 224 varyasyondan 74’ü tüm araçlarca destabilize edici bulunmuştur. Bu varyasyonlardan 29’u altı TKI’nin bağlanma afinitesini olumsuz etkilemiştir. Yabanıl tip proteinin bağlanma afiniteleri sırasıyla -10,7, -9,8, -10,6, -9,1, -10,8 ve -11,1 kcal/mol’dur. I242T ve V268M varyasyonları en zayıf bağlanma değerlerine sahipken, A350T, M351V, Y353S, L354Q, I360T ve H361R varyasyonları M351/F359 bölgesine yakınlıkları nedeniyle kritik bulunmuştur. Çoğu varyasyonlu görüntüde gerçekleştirilen kenetlenme T315 aminoasidi ile hidrojen bağı oluşturmuştur. ABL1 varyasyonları, TKI bağlanmasını zayıflatarak tedavi etkinliğini azaltabilir. M351 ve F359 bölgesindeki varyasyonlar potansiyel direnç mekanizmaları açısından klinik takipte öncelikli değerlendirilmelidir.

Anahtar Kelimeler

• ABL1 geni
• Tek Nükleotid Varyasyonu (SNV)
• Kronik Miyeloid Lösemi (KML)
• Tirozin Kinaz İnhibitörleri (TKI)
• Biyoenformatik Araçları

Evaluation of Single Nucleotide Variations in the Chronic Myeloid Leukemia (CML) Associated ABL1 Gene and the Efficacy of Tyrosine Kinase Inhibitors by Bioinformatics Tools

Öz

The ABL1 protein plays a critical role in the pathogenesis of chronic myeloid leukaemia (CML). In the treatment of CML, tyrosine kinase inhibitors (TKIs) targeting the ATP and myristoyl binding pockets of ABL1 are used. In this study, we aimed to evaluate the effects of missense variations in the ABL1 protein kinase domain on protein stability and TKI binding affinities. A total of 201 missense variations in the ABL1 protein kinase domain were examined, and 224 amino acid variations that could affect the ATP and myristoyl binding regions were analysed. Effects on protein stability were predicted using MAESTRO-web, I-Mutant 2.0, DUET, SDM, CUPSAT, and MUpro. Variants identified as destabilising in all tools were modelled using Swiss-Model DeepView, and binding affinities for Imatinib, Dasatinib, Nilotinib, Bosutinib, Ponatinib, and Asciminib were calculated using AutoDock Vina with wild-type ABL1 as a reference. Functional effects were determined using PolyPhen2, PHD-SNP, PredictProtein, and PANTHER. Of the 224 variations, 74 were found to be destabilising by all tools. Of these variations, 29 negatively affected the binding affinity of six TKIs. The binding affinities of the wild-type protein are -10.7, -9.8, -10.6, -9.1, -10.8, and -11.1 kcal/mol, respectively. The I242T and V268M variations had the weakest binding values, while the A350T, M351V, Y353S, L354Q, I360T, and H361R variations were considered critical due to their proximity to the M351/F359 region. Most of the docking performed on the variant structures formed a hydrogen bond with the T315 amino acid. ABL1 variants may weaken TKI binding, thereby reducing treatment efficacy. Variants in the M351 and F359 region should be prioritised for clinical monitoring in terms of potential resistance mechanisms.

Anahtar Kelimeler

• ABL1 gene
• Single Nucleotide Variation (SNV)
• Chronic Myeloid Leukemia (CML)
• Tyrosine Kinase Inhibitors (TKI)
• Bioinformatics Tools

Kaynakça

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