123
rms first mass out rms_IRB.out :15 Calculate
RMSD for all atoms of IRB (residue 15) and report the results in file rms_IRB.out
atomicfluct out fluct_CD.out :1- 14 Calculate RMS
fluctuations for the 2-HP-β-CD residues
Acknowledgments
This work has been co-financed by the European Union and Greek
national funds through the program “Support for Researchers
with Emphasis on Young Researchers” (call code: EDBM34, ΚΕ
14995) and under the research title “Preparation and study of
innovative forms of administration of pharmaceutical molecules
targeting at improved pharmacological properties.”
References
1. Hodgson J (2001) ADMET—turning chemicals into drugs. Nat Biotechnol 19(8):722–
726. https://doi.org/10.1038/90761
2. Kalepu S, Nekkanti V (2015) Insoluble drug
delivery strategies: review of recent advances
and business prospects. Acta Pharm Sin B
5(5):442–453. https://doi.org/10.1016/j.
apsb.2015.07.003
3. Loftsson
T,
Brewster
ME
(2010)
Pharmaceutical applications of cyclodextrins:
basic science and product development. J Pharm
Pharmacol 62(11):1607–1621. https://doi.
org/10.1111/j.2042-7158.2010.01030.x
4. Kellici TF, Tzakos AG, Mavromoustakos T
(2015) Rational drug design and synthesis of
molecules targeting the angiotensin II type 1
and type 2 receptors. Molecules 20(3):3868–
3897.
https://doi.org/10.3390/
molecules20033868
5. Hirlekar R, Kadam V (2009) Preformulation
study of the inclusion complex irbesartanbeta- cyclodextrin.
AAPS
PharmSciTech
10(1):276–281. https://doi.org/10.1208/
s12249-009-9206-5
6. Karplus M, Petsko GA (1990) Molecular
dynamics simulations in biology. Nature
347(6294):631–639.
https://doi.
org/10.1038/347631a0
7. Karplus M, McCammon JA (2002) Molecular
dynamics simulations of biomolecules. Nat
Struct Biol 9(9):646–652. https://doi.
org/10.1038/nsb0902-646
8. Miranda WE, Ngo VA, Perissinotti LL,
Noskov SY (2017) Computational membrane biophysics: from ion channel interactions with drugs to cellular function. Biochim
Biophys Acta Proteins Proteom 1865(11 Pt
B):1643–1653. https://doi.org/10.1016/j.
bbapap.2017.08.008
9. Kumari I, Sandhu P, Ahmed M, Akhter Y
(2017) Molecular dynamics simulations, challenges and opportunities: a biologist’s prospective. Curr Protein Pept Sci 18(11):1163–1179.
https://doi.org/10.2174/13892037186661
70622074741
10. van der Vaart A (2015) Coupled bindingbending- folding: the complex conformational
dynamics of protein-DNA binding studied
by atomistic molecular dynamics simulations. Biochim Biophys Acta 1850(5):1091–
1098.
https://doi.org/10.1016/j.
bbagen.2014.08.009
11. Boccellino M, Di Domenico M, Donniacuo
M, Bitti G, Gritti G, Ambrosio P, Quagliuolo
L, Rinaldi B (2018) AT1-receptor blockade: protective effects of irbesartan in cardiomyocytes under hypoxic stress. PLoS One
13(10):e0202297. https://doi.org/10.1371/
journal.pone.0202297
12. Cheng YZ, Yang SL, Wang JY, Ye M, Zhuo
XY, Wang LT, Chen H, Zhang H, Yang L
(2018) Irbesartan attenuates advanced glycation end products-mediated damage in
diabetes- associated osteoporosis through the
Molecular Dynamics and Drug Complexation with Cyclodextrins
rms first mass out rms_IRB.out :15 Calculate
RMSD for all atoms of IRB (residue 15) and report the results in file rms_IRB.out
atomicfluct out fluct_CD.out :1- 14 Calculate RMS
fluctuations for the 2-HP-β-CD residues
Acknowledgments
This work has been co-financed by the European Union and Greek
national funds through the program “Support for Researchers
with Emphasis on Young Researchers” (call code: EDBM34, ΚΕ
14995) and under the research title “Preparation and study of
innovative forms of administration of pharmaceutical molecules
targeting at improved pharmacological properties.”
References
1. Hodgson J (2001) ADMET—turning chemicals into drugs. Nat Biotechnol 19(8):722–
726. https://doi.org/10.1038/90761
2. Kalepu S, Nekkanti V (2015) Insoluble drug
delivery strategies: review of recent advances
and business prospects. Acta Pharm Sin B
5(5):442–453. https://doi.org/10.1016/j.
apsb.2015.07.003
3. Loftsson
T,
Brewster
ME
(2010)
Pharmaceutical applications of cyclodextrins:
basic science and product development. J Pharm
Pharmacol 62(11):1607–1621. https://doi.
org/10.1111/j.2042-7158.2010.01030.x
4. Kellici TF, Tzakos AG, Mavromoustakos T
(2015) Rational drug design and synthesis of
molecules targeting the angiotensin II type 1
and type 2 receptors. Molecules 20(3):3868–
3897.
https://doi.org/10.3390/
molecules20033868
5. Hirlekar R, Kadam V (2009) Preformulation
study of the inclusion complex irbesartanbeta- cyclodextrin.
AAPS
PharmSciTech
10(1):276–281. https://doi.org/10.1208/
s12249-009-9206-5
6. Karplus M, Petsko GA (1990) Molecular
dynamics simulations in biology. Nature
347(6294):631–639.
https://doi.
org/10.1038/347631a0
7. Karplus M, McCammon JA (2002) Molecular
dynamics simulations of biomolecules. Nat
Struct Biol 9(9):646–652. https://doi.
org/10.1038/nsb0902-646
8. Miranda WE, Ngo VA, Perissinotti LL,
Noskov SY (2017) Computational membrane biophysics: from ion channel interactions with drugs to cellular function. Biochim
Biophys Acta Proteins Proteom 1865(11 Pt
B):1643–1653. https://doi.org/10.1016/j.
bbapap.2017.08.008
9. Kumari I, Sandhu P, Ahmed M, Akhter Y
(2017) Molecular dynamics simulations, challenges and opportunities: a biologist’s prospective. Curr Protein Pept Sci 18(11):1163–1179.
https://doi.org/10.2174/13892037186661
70622074741
10. van der Vaart A (2015) Coupled bindingbending- folding: the complex conformational
dynamics of protein-DNA binding studied
by atomistic molecular dynamics simulations. Biochim Biophys Acta 1850(5):1091–
1098.
https://doi.org/10.1016/j.
bbagen.2014.08.009
11. Boccellino M, Di Domenico M, Donniacuo
M, Bitti G, Gritti G, Ambrosio P, Quagliuolo
L, Rinaldi B (2018) AT1-receptor blockade: protective effects of irbesartan in cardiomyocytes under hypoxic stress. PLoS One
13(10):e0202297. https://doi.org/10.1371/
journal.pone.0202297
12. Cheng YZ, Yang SL, Wang JY, Ye M, Zhuo
XY, Wang LT, Chen H, Zhang H, Yang L
(2018) Irbesartan attenuates advanced glycation end products-mediated damage in
diabetes- associated osteoporosis through the
Molecular Dynamics and Drug Complexation with Cyclodextrins