De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin

Soykan Agar; Barbaros Akkurt; Levent Alparslan

doi:10.18596/jotcsa.1406290

Araştırma Makalesi

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Kaynak Göster

Yıl 2024, Cilt: 11 Sayı: 2, 623 - 632, 15.05.2024

Soykan Agar Barbaros Akkurt Levent Alparslan

https://doi.org/10.18596/jotcsa.1406290

Öz

Kaynakça

1. Dong L, Hu S, Gao J. Discovering drugs to treat coronavirus disease 2019 (COVID-19). DD&T. 2020 Feb 29;14(1):58–60. Available from: <DOI>.
2. Commission NH, others. Guidelines for the Prevention, Diagnosis, and Treatment of Novel Coronavirus-Induced Pneumonia. National Health Commission, Beijing, China,; 2020.
3. Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of M pro from COVID-19 virus and discovery of its inhibitors [Internet]. Biochemistry; 2020 Feb [cited 2023 Nov 7]. Available from: <DOI>.
4. Senathilake K, Samarakoon S, Tennekoon K. Virtual Screening of Inhibitors Against Spike Glycoprotein of SARS-CoV-2: A Drug Repurposing Approach [Internet]. LIFE SCIENCES; 2020 Mar [cited 2023 Nov 7]. Available from: <DOI>.
5. Chan JFW, Yuan S, Kok KH, To KKW, Chu H, Yang J, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The Lancet. 2020 Feb;395(10223):514–23. Available from: <DOI>.
6. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020 Feb;395(10224):565–74. Available from: <DOI>.
7. Liu C, Zhou Q, Li Y, Garner LV, Watkins SP, Carter LJ, et al. Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases. ACS Cent Sci. 2020 Mar 25;6(3):315–31. Available from: <DOI>.
8. Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. Gallagher T, editor. J Virol. 2020 Mar 17;94(7):e00127-20. Available from: <DOI>.
9. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci. 2020 Mar;63(3):457–60. Available from: <DOI>.
10. Huentelman MJ, Zubcevic J, Hernández Prada JA, Xiao X, Dimitrov DS, Raizada MK, et al. Structure-Based Discovery of a Novel Angiotensin-Converting Enzyme 2 Inhibitor. Hypertension. 2004 Dec;44(6):903–6. Available from: <DOI>.
11. Khaerunnisa S, Kurniawan H, Awaluddin R, Suhartati S, Soetjipto S. Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study [Internet]. MEDICINE & PHARMACOLOGY; 2020 Mar [cited 2023 Nov 7]. Available from: <DOI>.
12. Chang KO, Kim Y, Lovell S, Rathnayake A, Groutas W. Antiviral Drug Discovery: Norovirus Proteases and Development of Inhibitors. Viruses. 2019 Feb 25;11(2):197. Available from: <DOI>.
13. Li JY, You Z, Wang Q, Zhou ZJ, Qiu Y, Luo R, et al. The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future. Microbes and Infection. 2020 Mar;22(2):80–5. Available from: <DOI>.
14. Delang L, Abdelnabi R, Neyts J. Favipiravir as a potential countermeasure against neglected and emerging RNA viruses. Antiviral Research. 2018 May;153:85–94. Available from: <DOI>.
15. Xu Z, Peng C, Shi Y, Zhu Z, Mu K, Wang X, et al. Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation [Internet]. Pharmacology and Toxicology; 2020 Jan [cited 2023 Nov 7]. Available from: <DOI>.
16. Gopal Samy B, Xavier L. Molecular docking studies on antiviral drugs for SARS. International Journal. 2015;5(3):75–9.
17. Peng C, Zhu Z, Shi Y, Wang X, Mu K, Yang Y, et al. Computational study of the strong binding mechanism of SARS-CoV-2 spike and ACE2 [Internet]. Chemistry; 2020 Feb [cited 2023 Feb 22]. Available from: <DOI>.
18. Copp DH, Cameron EC. Demonstration of a Hypocalcemic Factor (Calcitonin) in Commercial Parathyroid Extract. Science. 1961 Dec 22;134(3495):2038–2038. Available from: <DOI>.
19. Azria M, Copp DH, Zanelli JM. 25 Years of salmon calcitonin: From synthesis to therapeutic use. Calcif Tissue Int. 1995 Dec;57(6):405–8. Available from: <DOI>.
20. Woodrow J, Noseworthy C, Fudge N, Hoff A, Gagel R, Kovacs C. Calcitonin/calcitonin gene-related peptide protect the maternal skeleton from excessive resorption during lactation. Journal of bone and mineral research. 2003. p. S37–S37.
21. Hoff A, Thomas P, Cote G, Qiu H, Bain S, Puerner D, et al. Generation of a calcitonin knockout mouse model. Bone. 1998;23(suppl 5):S164.
22. Hirsch PF, Baruch H. Is Calcitonin an Important Physiological Substance? ENDO. 2003;21(3):201–8. Available from: <DOI>.
23. Hoff AO, Catala-Lehnen P, Thomas PM, Priemel M, Rueger JM, Nasonkin I, et al. Increased bone mass is an unexpected phenotype associated with deletion of the calcitonin gene. J Clin Invest. 2002 Dec 15;110(12):1849–57. Available from: <DOI>.
24. Zaidi M, Inzerillo AM, Troen B, Moonga BS, Abe E, Burckhardt P. Molecular and Clinical Pharmacology of Calcitonin. In: Principles of Bone Biology [Internet]. Elsevier; 2002 [cited 2023 Nov 7]. p. 1423–40. Available from: <DOI>.
25. Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide. Science. 1991 Dec 6;254(5037):1497–500. Available from: <DOI>.
26. Wittung P, Nielsen PE, Buchardt O, Egholm M, Nordén B. DNA-like double helix formed by peptide nucleic acid. Nature. 1994 Apr;368(6471):561–3. Available from: <DOI>.
27. Jensen KK, Ørum H, Nielsen PE, Nordén B. Kinetics for Hybridization of Peptide Nucleic Acids (PNA) with DNA and RNA Studied with the BIAcore Technique. Biochemistry. 1997 Apr 1;36(16):5072–7. Available from: <DOI>.
28. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules. Nature. 1993 Oct;365(6446):566–8. Available from: <DOI>.
29. Christensen L, Fitzpatrick R, Gildea B, Petersen KH, Hansen HF, Koch T, et al. Solid‐Phase synthesis of peptide nucleic acids. Journal of Peptide Science. 1995 May;1(3):175–83. Available from: <DOI>.
30. Dueholm KL, Egholm M, Behrens C, Christensen L, Hansen HF, Vulpius T, et al. Synthesis of peptide nucleic acid monomers containing the four natural nucleobases: thymine, cytosine, adenine, and guanine and their oligomerization. The Journal of Organic Chemistry. 1994;59(19):5767–73. Available from: <DOI>.
31. Thomson SA, Josey JA, Cadilla R, Gaul MD, Fred Hassman C, Luzzio MJ, et al. Fmoc mediated synthesis of Peptide Nucleic Acids. Tetrahedron. 1995 May;51(22):6179–94. Available from: <DOI>.
32. N. Ganesh K, E. Nielsen P. Peptide Nucleic Acids: Analogs and Derivatives. Current Organic Chemistry. 2000 Sep 1;4(9):931–43. Available from: <DOI>.
33. Eldrup AB, Dahl O, Nielsen PE. A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures. J Am Chem Soc. 1997 Nov 1;119(45):11116–7. Available from: <DOI>.
34. Ljungstrøm T, Knudsen H, Nielsen PE. Cellular Uptake of Adamantyl Conjugated Peptide Nucleic Acids. Bioconjugate Chem. 1999 Nov 1;10(6):965–72. Available from: <DOI>.
35. Cutrona G, Carpaneto EM, Ulivi M, Roncella S, Landt O, Ferrarini M, et al. Effects in live cells of a c-myc anti-gene PNA linked to a nuclear localization signal. Nat Biotechnol. 2000 Mar;18(3):300–3. Available from: <DOI>.
36. Mologni L. Additive antisense effects of different PNAs on the in vitro translation of the PML/RARalpha gene. Nucleic Acids Research. 1998 Apr 15;26(8):1934–8. Available from: <DOI>.
37. Mayhood T, Kaushik N, Pandey PK, Kashanchi F, Deng L, Pandey VN. Inhibition of Tat-Mediated Transactivation of HIV-1 LTR Transcription by Polyamide Nucleic Acid Targeted to TAR Hairpin Element. Biochemistry. 2000 Sep 1;39(38):11532–9. Available from: <DOI>.
38. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 09, Revision D.01. Wallingford, CT: Gaussian, Inc.; 2009.
39. Becke A. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J Chem Phys. 1993;98:5648–52.
40. Dennington R, Keith TA, Millam JM. GaussView 5.0. Wallingford, CT: Gaussian, Inc.; 2009.
41. Gaillard T. Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark. J Chem Inf Model. 2018 Aug 27;58(8):1697–706. Available from: <DOI>.
42. Şenel P, Agar S, İş YS, Altay F, Gölcü A, Yurtsever M. Deciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies. Journal of Pharmaceutical and Biomedical Analysis. 2022 Feb;209:114490. Available from: <DOI>.
43. Cheraghi S, Şenel P, Dogan Topal B, Agar S, Majidian M, Yurtsever M, et al. Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques. Biosensors. 2023 Feb 21;13(3):300. Available from: <DOI>.
44. Desmond D. Shaw Research: New York. NY; 2017.
45. Evans DJ, Holian BL. The Nose–Hoover thermostat. The Journal of Chemical Physics. 1985 Oct 15;83(8):4069–74. Available from: <DOI>.
46. Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics. 1994 Sep 1;101(5):4177–89. Available from: <DOI>.
47. Mestre B, Arzumanov A, Singh M, Boulmé F, Litvak S, Gait MJ. Oligonucleotide inhibition of the interaction of HIV-1 Tat protein with the trans-activation responsive region (TAR) of HIV RNA. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Apr;1445(1):86–98. Available from: <DOI>.
48. Mhashilkar AM, Biswas DK, LaVecchio J, Pardee AB, Marasco WA. Inhibition of human immunodeficiency virus type 1 replication in vitro by a novel combination of anti-Tat single-chain intrabodies and NF-kappa B antagonists. J Virol. 1997 Sep;71(9):6486–94. Available from: <DOI>.
49. Hirschman SZ, Chen CW. Peptide nucleic acids stimulate gamma interferon and inhibit the replication of the human immunodeficiency virus. J Investig Med. 1996 Aug;44(6):347–51. Available from: <URL>.
50. Alparslan AL, Yildiz Türkyilmaz G, Kozaci LD, Karasulu E. Thermoreversible Gel Formulation for the Intranasal Delivery of Salmon Calcitonin and Comparison Studies of In Vivo Bioavailability. tjps. 2023 Jun 1;20(3):127–40. Available from: <DOI>.
51. Şenel P, Agar S, Sayin VO, Altay F, Yurtsever M, Gölcü A. Elucidation of binding interactions and mechanism of Fludarabine with dsDNA via multispectroscopic and molecular docking studies. Journal of Pharmaceutical and Biomedical Analysis. 2020 Feb;179:112994. Available from: <DOI>.

De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin

Yıl 2024, Cilt: 11 Sayı: 2, 623 - 632, 15.05.2024

Soykan Agar Barbaros Akkurt Levent Alparslan

https://doi.org/10.18596/jotcsa.1406290

Öz

De novo drug design has been studied utilizing the organic chemical structures of Salmon Calcitonin 9 - 19 and Peptide Nucleic Acid (PNA) to suppress Coronavirus Ribonucleic Acid (RNA)-Glycoprotein complex. PNA has a polyamide backbone and Thymine pendant groups to selectively bind and inhibit Adenine domains of the RNA-Glycoprotein complex. While doing so, molecular docking and molecular dynamics studies revealed that there is great inhibition docking energy (-12.1 kcal/mol) with significantly good inhibition constant (124.1 µM) values confirming the efficient nucleotide-specific silencing of Coronavirus RNA-Glycoprotein complex.

Anahtar Kelimeler

Salmon Calcitonin, Coronavirus RNA, Coronavirus Glycoprotein, Molecular Docking, Molecular Dynamics, Hydrogen Contact Mapping

Kaynakça

1. Dong L, Hu S, Gao J. Discovering drugs to treat coronavirus disease 2019 (COVID-19). DD&T. 2020 Feb 29;14(1):58–60. Available from: <DOI>.
2. Commission NH, others. Guidelines for the Prevention, Diagnosis, and Treatment of Novel Coronavirus-Induced Pneumonia. National Health Commission, Beijing, China,; 2020.
3. Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of M pro from COVID-19 virus and discovery of its inhibitors [Internet]. Biochemistry; 2020 Feb [cited 2023 Nov 7]. Available from: <DOI>.
4. Senathilake K, Samarakoon S, Tennekoon K. Virtual Screening of Inhibitors Against Spike Glycoprotein of SARS-CoV-2: A Drug Repurposing Approach [Internet]. LIFE SCIENCES; 2020 Mar [cited 2023 Nov 7]. Available from: <DOI>.
5. Chan JFW, Yuan S, Kok KH, To KKW, Chu H, Yang J, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The Lancet. 2020 Feb;395(10223):514–23. Available from: <DOI>.
6. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020 Feb;395(10224):565–74. Available from: <DOI>.
7. Liu C, Zhou Q, Li Y, Garner LV, Watkins SP, Carter LJ, et al. Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases. ACS Cent Sci. 2020 Mar 25;6(3):315–31. Available from: <DOI>.
8. Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. Gallagher T, editor. J Virol. 2020 Mar 17;94(7):e00127-20. Available from: <DOI>.
9. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci. 2020 Mar;63(3):457–60. Available from: <DOI>.
10. Huentelman MJ, Zubcevic J, Hernández Prada JA, Xiao X, Dimitrov DS, Raizada MK, et al. Structure-Based Discovery of a Novel Angiotensin-Converting Enzyme 2 Inhibitor. Hypertension. 2004 Dec;44(6):903–6. Available from: <DOI>.
11. Khaerunnisa S, Kurniawan H, Awaluddin R, Suhartati S, Soetjipto S. Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study [Internet]. MEDICINE & PHARMACOLOGY; 2020 Mar [cited 2023 Nov 7]. Available from: <DOI>.
12. Chang KO, Kim Y, Lovell S, Rathnayake A, Groutas W. Antiviral Drug Discovery: Norovirus Proteases and Development of Inhibitors. Viruses. 2019 Feb 25;11(2):197. Available from: <DOI>.
13. Li JY, You Z, Wang Q, Zhou ZJ, Qiu Y, Luo R, et al. The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future. Microbes and Infection. 2020 Mar;22(2):80–5. Available from: <DOI>.
14. Delang L, Abdelnabi R, Neyts J. Favipiravir as a potential countermeasure against neglected and emerging RNA viruses. Antiviral Research. 2018 May;153:85–94. Available from: <DOI>.
15. Xu Z, Peng C, Shi Y, Zhu Z, Mu K, Wang X, et al. Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation [Internet]. Pharmacology and Toxicology; 2020 Jan [cited 2023 Nov 7]. Available from: <DOI>.
16. Gopal Samy B, Xavier L. Molecular docking studies on antiviral drugs for SARS. International Journal. 2015;5(3):75–9.
17. Peng C, Zhu Z, Shi Y, Wang X, Mu K, Yang Y, et al. Computational study of the strong binding mechanism of SARS-CoV-2 spike and ACE2 [Internet]. Chemistry; 2020 Feb [cited 2023 Feb 22]. Available from: <DOI>.
18. Copp DH, Cameron EC. Demonstration of a Hypocalcemic Factor (Calcitonin) in Commercial Parathyroid Extract. Science. 1961 Dec 22;134(3495):2038–2038. Available from: <DOI>.
19. Azria M, Copp DH, Zanelli JM. 25 Years of salmon calcitonin: From synthesis to therapeutic use. Calcif Tissue Int. 1995 Dec;57(6):405–8. Available from: <DOI>.
20. Woodrow J, Noseworthy C, Fudge N, Hoff A, Gagel R, Kovacs C. Calcitonin/calcitonin gene-related peptide protect the maternal skeleton from excessive resorption during lactation. Journal of bone and mineral research. 2003. p. S37–S37.
21. Hoff A, Thomas P, Cote G, Qiu H, Bain S, Puerner D, et al. Generation of a calcitonin knockout mouse model. Bone. 1998;23(suppl 5):S164.
22. Hirsch PF, Baruch H. Is Calcitonin an Important Physiological Substance? ENDO. 2003;21(3):201–8. Available from: <DOI>.
23. Hoff AO, Catala-Lehnen P, Thomas PM, Priemel M, Rueger JM, Nasonkin I, et al. Increased bone mass is an unexpected phenotype associated with deletion of the calcitonin gene. J Clin Invest. 2002 Dec 15;110(12):1849–57. Available from: <DOI>.
24. Zaidi M, Inzerillo AM, Troen B, Moonga BS, Abe E, Burckhardt P. Molecular and Clinical Pharmacology of Calcitonin. In: Principles of Bone Biology [Internet]. Elsevier; 2002 [cited 2023 Nov 7]. p. 1423–40. Available from: <DOI>.
25. Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide. Science. 1991 Dec 6;254(5037):1497–500. Available from: <DOI>.
26. Wittung P, Nielsen PE, Buchardt O, Egholm M, Nordén B. DNA-like double helix formed by peptide nucleic acid. Nature. 1994 Apr;368(6471):561–3. Available from: <DOI>.
27. Jensen KK, Ørum H, Nielsen PE, Nordén B. Kinetics for Hybridization of Peptide Nucleic Acids (PNA) with DNA and RNA Studied with the BIAcore Technique. Biochemistry. 1997 Apr 1;36(16):5072–7. Available from: <DOI>.
28. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules. Nature. 1993 Oct;365(6446):566–8. Available from: <DOI>.
29. Christensen L, Fitzpatrick R, Gildea B, Petersen KH, Hansen HF, Koch T, et al. Solid‐Phase synthesis of peptide nucleic acids. Journal of Peptide Science. 1995 May;1(3):175–83. Available from: <DOI>.
30. Dueholm KL, Egholm M, Behrens C, Christensen L, Hansen HF, Vulpius T, et al. Synthesis of peptide nucleic acid monomers containing the four natural nucleobases: thymine, cytosine, adenine, and guanine and their oligomerization. The Journal of Organic Chemistry. 1994;59(19):5767–73. Available from: <DOI>.
31. Thomson SA, Josey JA, Cadilla R, Gaul MD, Fred Hassman C, Luzzio MJ, et al. Fmoc mediated synthesis of Peptide Nucleic Acids. Tetrahedron. 1995 May;51(22):6179–94. Available from: <DOI>.
32. N. Ganesh K, E. Nielsen P. Peptide Nucleic Acids: Analogs and Derivatives. Current Organic Chemistry. 2000 Sep 1;4(9):931–43. Available from: <DOI>.
33. Eldrup AB, Dahl O, Nielsen PE. A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures. J Am Chem Soc. 1997 Nov 1;119(45):11116–7. Available from: <DOI>.
34. Ljungstrøm T, Knudsen H, Nielsen PE. Cellular Uptake of Adamantyl Conjugated Peptide Nucleic Acids. Bioconjugate Chem. 1999 Nov 1;10(6):965–72. Available from: <DOI>.
35. Cutrona G, Carpaneto EM, Ulivi M, Roncella S, Landt O, Ferrarini M, et al. Effects in live cells of a c-myc anti-gene PNA linked to a nuclear localization signal. Nat Biotechnol. 2000 Mar;18(3):300–3. Available from: <DOI>.
36. Mologni L. Additive antisense effects of different PNAs on the in vitro translation of the PML/RARalpha gene. Nucleic Acids Research. 1998 Apr 15;26(8):1934–8. Available from: <DOI>.
37. Mayhood T, Kaushik N, Pandey PK, Kashanchi F, Deng L, Pandey VN. Inhibition of Tat-Mediated Transactivation of HIV-1 LTR Transcription by Polyamide Nucleic Acid Targeted to TAR Hairpin Element. Biochemistry. 2000 Sep 1;39(38):11532–9. Available from: <DOI>.
38. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 09, Revision D.01. Wallingford, CT: Gaussian, Inc.; 2009.
39. Becke A. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J Chem Phys. 1993;98:5648–52.
40. Dennington R, Keith TA, Millam JM. GaussView 5.0. Wallingford, CT: Gaussian, Inc.; 2009.
41. Gaillard T. Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark. J Chem Inf Model. 2018 Aug 27;58(8):1697–706. Available from: <DOI>.
42. Şenel P, Agar S, İş YS, Altay F, Gölcü A, Yurtsever M. Deciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies. Journal of Pharmaceutical and Biomedical Analysis. 2022 Feb;209:114490. Available from: <DOI>.
43. Cheraghi S, Şenel P, Dogan Topal B, Agar S, Majidian M, Yurtsever M, et al. Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques. Biosensors. 2023 Feb 21;13(3):300. Available from: <DOI>.
44. Desmond D. Shaw Research: New York. NY; 2017.
45. Evans DJ, Holian BL. The Nose–Hoover thermostat. The Journal of Chemical Physics. 1985 Oct 15;83(8):4069–74. Available from: <DOI>.
46. Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics. 1994 Sep 1;101(5):4177–89. Available from: <DOI>.
47. Mestre B, Arzumanov A, Singh M, Boulmé F, Litvak S, Gait MJ. Oligonucleotide inhibition of the interaction of HIV-1 Tat protein with the trans-activation responsive region (TAR) of HIV RNA. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Apr;1445(1):86–98. Available from: <DOI>.
48. Mhashilkar AM, Biswas DK, LaVecchio J, Pardee AB, Marasco WA. Inhibition of human immunodeficiency virus type 1 replication in vitro by a novel combination of anti-Tat single-chain intrabodies and NF-kappa B antagonists. J Virol. 1997 Sep;71(9):6486–94. Available from: <DOI>.
49. Hirschman SZ, Chen CW. Peptide nucleic acids stimulate gamma interferon and inhibit the replication of the human immunodeficiency virus. J Investig Med. 1996 Aug;44(6):347–51. Available from: <URL>.
50. Alparslan AL, Yildiz Türkyilmaz G, Kozaci LD, Karasulu E. Thermoreversible Gel Formulation for the Intranasal Delivery of Salmon Calcitonin and Comparison Studies of In Vivo Bioavailability. tjps. 2023 Jun 1;20(3):127–40. Available from: <DOI>.
51. Şenel P, Agar S, Sayin VO, Altay F, Yurtsever M, Gölcü A. Elucidation of binding interactions and mechanism of Fludarabine with dsDNA via multispectroscopic and molecular docking studies. Journal of Pharmaceutical and Biomedical Analysis. 2020 Feb;179:112994. Available from: <DOI>.

Toplam 51 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	İngilizce
Konular	Hesaplamalı Kimya
Bölüm	ARAŞTIRMA MAKALELERİ
Yazarlar	Soykan Agar 0000-0002-9870-6882 Barbaros Akkurt 0000-0003-4066-3004 Levent Alparslan 0000-0003-0113-6850
Yayımlanma Tarihi	15 Mayıs 2024
Gönderilme Tarihi	18 Aralık 2023
Kabul Tarihi	29 Ocak 2024
Yayımlandığı Sayı	Yıl 2024 Cilt: 11 Sayı: 2

Kaynak Göster

Vancouver	Agar S, Akkurt B, Alparslan L. De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin. JOTCSA. 2024;11(2):623-32.

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