fa مطالعه In-Silico اتصال آپتامر-سافرانال با استفاده از داکینگ مولکولی و شبیه‌سازی دینامیک مولکولی صنايع غذايي Food Science پژوهشي Research <span style="font-size:10pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><span b="" lang="AR-SA" style="font-family:" titr="">سابقه و هدف:</span> <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">در این مطالعه</span></span> <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">از داکینگ و شبیه&shy;سازی دینامیک مولکولی برای آنالیز برهم&shy;کنش&shy;های پیوندی میان سافرانال، یک ماده شیمیایی زیست‌فعال حاصل از زعفران و آپتامرهای </span></span>ssDNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> و </span></span>ssRNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> استفاده گردید. </span></span><span lang="AR-SA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">هدف اصلی، شناسایی آپتامرهای مناسب با قابلیت اتصال مؤثر به سافرانال، با تأکید بر تعیین تمایل پیوندی و پایداری دینامیکی بود.</span></span><span lang="FA" style="font-size:11.0pt"><span style="font-family:"B Nazanin""></span></span></span></span></span></span><br> <span style="font-size:10pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><span b="" lang="AR-SA" style="font-family:" titr="">مواد و روش</span><span dir="LTR" style="font-size:9.0pt">‌</span><span b="" lang="AR-SA" style="font-family:" titr="">ها:</span> <span lang="AR-SA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">داکینگ مولکولی با استفاده از </span></span>AutoDock Tools 1.5.7 <span lang="AR-SA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">بر روی آپتامرهای انتخابی </span></span>ssDNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> (شناسه&shy;های</span></span> PDB<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">= </span></span>6J2W<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">، </span></span>7QB3<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> و </span></span>2L5K<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">) و آپتامرهای </span></span>ssRNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> (شناسه&shy;های</span></span> PDB<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">= </span></span>6V9B<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> و </span></span>8D2B<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">)</span></span><span lang="AR-SA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> انجام شد. </span></span><span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">پس از داکینگ مولکولی، از </span></span>GROMACS 2020.1 <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">برای انجام شبیه‌سازی دینامیک مولکولی به مدت 200 نانوثانیه برای دو آپتامر کاندید استفاده شد تا پایداری کمپلکس‌های آپتامر-لیگاند بررسی گردد.</span></span><span lang="AR-SA" style="font-size:11.0pt"><span style="font-family:"B Nazanin""></span></span></span></span></span></span><br> <span style="font-size:10pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><span b="" lang="AR-SA" style="font-family:" titr="">یافته</span><span dir="LTR" style="font-size:9.0pt">‌</span><span b="" lang="AR-SA" style="font-family:" titr="">ها</span><span dir="LTR" style="font-size:9.0pt">‌</span><span b="" lang="AR-SA" style="font-family:" titr="">:</span> <span lang="AR-SA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">طبق </span></span><span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">نتایج داکینگ مولکولی، </span></span>&Delta;G<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> برای آپتامرهای </span></span>6J2W<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">، </span></span>7QB3<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> و </span></span>2L5K<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> به ترتیب 85/4-، 39/4- و 53/4- کیلوکالری بر مول و برای آپتامرهای </span></span>6V9B<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> و </span></span>8D2B <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">به ترتیب 27/5- و 31/5- کیلوکالری بر مول به دست آمد. آپتامر </span></span>ssRNA 8D2B <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">بهترین عملکرد را داشت. آپتامر </span></span>ssDNA 6J2W<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> نیز به دلیل کمترین </span></span>&Delta;G<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> انتخاب گردید. در شبیه&shy;سازی دینامیک مولکولی، آپتامر </span></span>ssRNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> نوسانات قابل توجهی در</span></span> RMSD<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> پس از 40 نانوثانیه نشان داد و به ناپایداری در تعامل با سافرانال رسید، درحالی&shy;که آپتامر </span></span>ssDNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> پایداری بیشتری داشت. نتایج </span></span>RMSF<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> نشان داد که برهم&shy;کنش </span></span>ssRNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">-سافرانال نوسانات بالاتری نسبت به </span></span>ssRNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> مرجع دارد.</span></span><span lang="FA" style="font-size:11.0pt"><span style="font-family:"B Nazanin""></span></span></span></span></span></span><br> <span style="font-size:10pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><span b="" lang="AR-SA" style="font-family:" titr="">نتیجه گیری:</span> <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">آپتامر </span></span>ssDNA<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:"> (</span></span>6J2W<span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">)</span></span> <span lang="FA" style="font-size:12.0pt"><span b="" nazanin="" style="font-family:">به عنوان گزینه‌ای مناسب برای توسعه حسگرهای مبتنی بر آپتامر پیشنهاد می&shy;شود، اما برای تأیید اثربخشی آن، نیاز به اعتبارسنجی تجربی می&shy;باشد. این مطالعه می‌تواند به پایش کیفیت و خلوص زعفران کمک نماید.</span></span><span lang="AR-SA" style="font-size:11.0pt"><span style="font-family:"B Nazanin""></span></span></span></span></span></span><br> &nbsp; <span style="font-size:10pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b>Background and Objective:</b> In this work, the binding interactions between ssDNA and ssRNA aptamers and safranal, a bioactive substance produced from saffron, were examined using molecular docking and dynamics simulations. The main objective was to find appropriate aptamers that could bind safranal effectively, with an emphasis on dynamic stability and binding affinity.</span></span></span><br> <span style="font-size:10pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b>Materials and Methods:</b> ssRNA and ssDNA aptamers with PDB IDs of 6V9B and 8D2B and 6J2W, 7QB3, and 2L5K, respectively, were subjected to molecular docking using AutoDock Tools 1.5.7. Following molecular docking, two candidate aptamers were subjected to 200 ns of molecular dynamics simulation using GROMACS 2020.1, which was employed to evaluate the stability of aptamer-ligand complexes.</span></span></span><br> <span style="font-size:10pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b>Findings:</b> According to molecular docking results, the &Delta;G values for aptamers 6J2W, 7QB3, and 2L5K were determined to be -4.85, -4.39, and -4.53 kcal/mol, respectively, while the values for aptamers 6V9B and 8D2B were -5.27 and -5.31 kcal/mol. Among the ssRNA aptamers, 8D2B performed the best. The lowest &Delta;G value of the ssDNA aptamer 6J2W also led to its selection. The ssDNA aptamer exhibited higher stability in the molecular dynamics simulation, while the ssRNA aptamer showed notable fluctuations in RMSD after 40 ns and reached instability in interaction with safranal. The ssRNA-safranal interaction exhibited higher fluctuations , according to the RMSF results, than the reference ssRNA.</span></span></span><br> <span style="font-size:10pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b>Conclusion:</b> The ssDNA aptamer (6J2W) is proposed as a potential option to develop aptamer-based sensors; nevertheless, further experimental validation is required to confirm its effectiveness. The quality and purity of saffron can be monitored with the use of this study.</span></span></span> سافرانال, آپتامر, داکینگ مولکولی, شبیه سازی دینامیک مولکولی, زیست حسگر Safranal, Aptamer, Molecular Docking, Molecular Dynamics Simulation, Biosensor 57 68 http://nsft.sbmu.ac.ir/browse.php?a_code=A-10-4720-1&slc_lang=fa&sid=1 Z Mohammadi زهرا محمدی mohhammadizara1991@yahoo.com 11500319475328460027842 11500319475328460027842 No Gorgan University of Agricultural Sciences and Natural Resources دانشگاه علوم کشاورزی و منابع طبیعی گرگان M Jafari سید مهدی جعفری smjafari@gau.ac.ir 11500319475328460027843 11500319475328460027843 Yes Gorgan University of Agricultural Sciences and Natural Resources دانشگاه علوم کشاورزی و منابع طبیعی گرگان M Kashaninejad مهدی کاشانی نژاد kashani@gau.ac.ir 11500319475328460027844 11500319475328460027844 No Gorgan University of Agricultural Sciences and Natural Resources دانشگاه علوم کشاورزی و منابع طبیعی گرگان