Identification of Potential c-MET Inhibitors from Natural Product Library by Virtual Screening, Molecular Dynamics and MM/PBSA Approach

Abstract

c-MET is a transmembrane receptor tyrosine kinase and an important therapeutic target for anticancer drug development. Dysregulation of the c-MET/HGF pathway has been implicated in various human proliferative disorders. Crizotinib, initially developed as a selective c-MET inhibitor, is now recognized as a multitargeted tyrosine kinase inhibitor (TKI). Natural products remain a valuable source for drug discovery. In this study, a total of 153,019 natural product and natural product-like molecules collected from eight major libraries were screened to identify novel c-MET inhibitors using an integrated workflow combining virtual screening, ADME/toxicity filtering, molecular dynamics (MD) simulations, and MM/PBSA free energy analysis. A total of 30,534 molecules passing the Lipinski, PAINS and Brenk filters in the KNIME workflow were used in the virtual screening. After filtration based on the Veber, Egan, Ghose, and Muegge criteria, 148 molecules exhibited better binding scores than Crizotinib (−10.40 kcal/mol). Molecules with binding energies lower than –10.40 kcal/mol were carried forward for further analyses. Subsequent ProTox-II screening reduced the pool to seven non-toxic candidates. The two molecules among the selected seven that exhibited the highest binding scores were ZINC98363582 and ZINC98365604, each with a value of –10.70 kcal/mol. MD simulations (30 ns) demonstrated that all protein–ligand complexes maintained structural stability, showing average RMSD values between 0.125–0.20 nm, comparable to or better than the Crizotinib complex. MM/PBSA calculations revealed that several candidates exhibited markedly superior binding affinities relative to Crizotinib (−47.648 kJ/mol). Notably, ZINC98063878 displayed the strongest binding free energy (−153.481 kJ/mol), followed by NPA009357 (−112.425 kJ/mol) and NPA032454 (−109.835 kJ/mol). These values indicate significantly enhanced thermodynamic favorability driven by strong van der Waals and electrostatic contributions. Overall, the molecules ZINC98063878, NPA009357, NPA032454, ZINC98363582, and ZINC98365604 emerged as promising natural product-derived c-MET inhibitor candidates, outperforming the clinical reference molecule (Crizotinib) in both stability and predicted binding energy. These findings highlight their potential for further in vitro and in vivo evaluation toward developing next-generation c-MET–targeted anticancer agents.

Keywords

• ADME
• c-MET
• MM/PBSA
• molecular dynamics simulations
• natural products
• virtual screening

Sanal Tarama, Moleküler Dinamik ve MM/PBSA Yaklaşımı ile Doğal Ürün Kütüphanesinden Potansiyel c-MET İnhibitörlerinin Belirlenmesi

Abstract

c-MET, transmembran bir reseptör tirozin kinaz olup antikanser ilaç geliştirme için önemli bir terapötik hedeftir. c-MET/HGF yolaklarının düzensizliği çeşitli insan proliferatif bozukluklarıyla ilişkilendirilmiştir. Başlangıçta seçici bir c-MET inhibitörü olarak geliştirilen Crizotinib günümüzde çok hedefli bir tirozin kinaz inhibitörü (TKI) olarak bilinmektedir. Doğal ürünler, ilaç keşfinde hâlâ değerli bir kaynak oluşturmaktadır. Bu çalışmada, sekiz büyük kütüphaneden toplanan toplam 153.019 doğal ürün ve doğal ürün benzeri molekül, sanal tarama, ADME/toksisite filtreleme, moleküler dinamik (MD) simülasyonları ve MM/PBSA serbest enerji analizini birleştiren entegre bir iş akışı ile taranarak yeni c-MET inhibitörlerinin belirlenmesi amaçlanmıştır. KNIME iş akışında Lipinski, PAINS ve Brenk filtrelerinden geçen toplam 30.534 molekül sanal taramada kullanılmıştır. Veber, Egan, Ghose ve Muegge kriterlerine göre yapılan filtrasyonun ardından 148 molekül, Crizotinib’ten (−10.40 kcal/mol) daha iyi bağlanma skorları göstermiştir. Bağlanma enerjisi –10.40 kcal/mol’den daha düşük olan moleküller ileri analizlere taşınmıştır. Ardından yapılan ProTox-II taraması, havuzu yedi toksik olmayan adaya düşürmüştür. Seçilen yedi molekül arasında en yüksek bağlanma skoruna sahip olan iki molekül, her biri –10.70 kcal/mol değeri ile ZINC98363582 ve ZINC98365604 olmuştur. MD simülasyonları (30 ns), tüm protein–ligand komplekslerinin yapısal kararlılığını koruduğunu ve ortalama RMSD değerlerinin 0.125–0.20 nm arasında olduğunu göstermiştir; bu değerler Crizotinib kompleksine eşdeğer veya daha iyidir. MM/PBSA hesaplamaları, bazı adayların Crizotinib’e (−47.648 kJ/mol) kıyasla belirgin şekilde daha yüksek bağlanma afiniteleri gösterdiğini ortaya koymuştur. Özellikle ZINC98063878 en güçlü bağlanma serbest enerjisini (−153.481 kJ/mol) göstermiştir; bunu NPA009357 (−112.425 kJ/mol) ve NPA032454 (−109.835 kJ/mol) izlemiştir. Bu değerler, güçlü van der Waals ve elektrostatik katkılarla yönlendirilen belirgin şekilde artmış termodinamik elverişliliğe işaret etmektedir. Genel olarak, ZINC98063878, NPA009357, NPA032454, ZINC98363582 ve ZINC98365604 molekülleri hem kararlılık hem de tahmin edilen bağlanma enerjisi açısından klinik referans molekül olan Crizotinib'i geride bırakarak umut vadeden doğal ürün türevli c-MET inhibitörü adayları olarak öne çıkmıştır. Bu bulgular, bu moleküllerin yeni nesil c-MET hedefli antikanser ajanların geliştirilmesi amacıyla ileri in vitro ve in vivo değerlendirmeler için potansiyel taşıdığını göstermektedir.

Keywords

• ADME
• c-MET
• doğal ürünler
• MM/PBSA
• moleküler dinamik simülasyonları
• sanal tarama

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