طراحی و شبیه‌سازی نانو لینکرهای پلی‌کاتیونی برای اتصال پلی‌آنیون‌ها به یکدیگر

نوع مقاله : مقاله علمی

نویسندگان
1 دانشجوی دکتری گروه مهندسی مکانیک ،دانشگاه فردوسی مشهد
2 گروه مهندسی مکانیک، دانشگاه فردوسی مشهد، مشهد، ایران
3 گروه مهندسی مکانیک، دانشگاه حکیم سبزواری، سبزوار، ایران
چکیده
در این مقاله، نانولینکرهای پلی‌کاتیونی جدیدی برای اتصال پلی‌آنیون‌ها طراحی و با استفاده از شبیه‌سازی دینامیک مولکولی بررسی شده‌اند. دو نوع لینکر چندشاخه‌ای با هسته مرکزی اسید پالمیتیک و شاخه‌های اسپرمیدین طراحی و بهینه‌سازی شدند: یکی با هشت شاخه و دیگری با شش شاخه اسپرمیدین. پایداری این لینکرها در سه دمای مختلف طی 20 نانوثانیه شبیه‌سازی شد و نتایج نشان داد که هر دو ساختار پایدار باقی می‌مانند. به‌منظور ارزیابی قابلیت اتصال این لینکرها، پلی‌آنیون‌های DNA اریگامی و هپارین به‌عنوان نمونه انتخاب شدند. پس از تشکیل کمپلکس میان لینکرها و این ساختارها، شبیه‌سازی‌های دینامیک مولکولی انجام شد. نتایج نشان داد که کمپلکس‌ها از پایداری بالایی برخوردارند و تعاملات بین‌مولکولی قوی، به‌ویژه در انرژی‌های الکترواستاتیک و واندروالس، مشاهده شد. به‌طورکلی، یافته‌های این مطالعه نشان می‌دهند که نانولینکرهای پلی‌کاتیونی پیشنهادی پتانسیل بالایی برای اتصال و تثبیت پلی‌آنیون‌ها دارند و می‌توانند در حوزه‌هایی مانند دارورسانی هدفمند، ژن‌درمانی، مهندسی بافت، تشخیص بیماری و نانو فناوری مورد استفاده قرار گیرند.
کلیدواژه‌ها
موضوعات

عنوان مقاله English

Design and Simulation of Polycationic Nano-Linkers for Connecting Polyanions Together

نویسندگان English

Sadegh Dastorani 1
Mahmoud Shariati 2
Reza Hasanzadeh Ghasemi 3
1 PhD Candidate, Department of Mechanical Engineering, Ferdowsi University of Mashhad
2 Department of Mechanical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
3 Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
چکیده English

This study presents the design and molecular dynamics (MD) simulation of novel polycationic nano-linkers for connecting polyanions. Two types of multi-branched linkers were designed, featuring a palmitic acid core and spermidine branches: one with eight spermidine branches and the other with six. The stability of these linkers was assessed over 20 nanoseconds at three different temperatures, confirming their structural integrity. To evaluate their binding capability, two polyanions—DNA origami and heparin—were selected as model systems. Following complex formation between the linkers and these polyanions, MD simulations were performed. The results demonstrated high stability in the complexes, with strong intermolecular interactions, particularly in electrostatic and van der Waals energies. The designed polycationic nano-linkers exhibited robust binding to both DNA origami and heparin, forming stable complexes without significant structural deviations. Root-mean-square deviation (RMSD) analysis confirmed structural stability across varying temperatures (300 K, 310 K, and 320 K), indicating their potential for biomedical applications under physiological conditions. Energy decomposition analysis revealed that the octa-branched linker (Linker 1) exhibited stronger interactions due to its higher number of cationic branches, while the hexa-branched linker (Linker 2) also demonstrated effective binding. These findings suggest that the proposed polycationic nano-linkers are promising candidates for connecting polyanions in applications such as targeted drug delivery, gene therapy, tissue engineering, disease diagnostics, and nanotechnology. The study highlights the importance of computational modeling in optimizing nanoscale molecular interactions for biomedical advancements.

کلیدواژه‌ها English

Polycationic nano-linker
DNA origami
Heparin
Molecular dynamics simulation
Spermidine
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