Limits...
Molecular umbrella conjugate for the ocular delivery of siRNA.

Janout V, Cline LL, Feuston BP, Klein L, O'Brien A, Tucker T, Yuan Y, O'Neill-Davis LA, Peiffer RL, Nerurkar SS, Jadhav V, Tellers DM, Regen SL - Bioconjug. Chem. (2014)

Bottom Line: The synthesis, computer modeling, and biological activity of an octawalled molecular umbrella short interfacing RNA (siRNA) conjugate is described.This molecular umbrella-siRNA conjugate exhibited mRNA knockdown activity in vitro in the absence of a transfection reagent.Evaluation of this molecular umbrella conjugate in vivo, using the rat eye via intravitreal injection, resulted in sequence specific mRNA knockdown in the retina with no obvious signs of toxicity, as judged by ophthalmic examination.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Lehigh University , Bethlehem, Pennsylvania 18015, United States.

ABSTRACT
The synthesis, computer modeling, and biological activity of an octawalled molecular umbrella short interfacing RNA (siRNA) conjugate is described. This molecular umbrella-siRNA conjugate exhibited mRNA knockdown activity in vitro in the absence of a transfection reagent. Evaluation of this molecular umbrella conjugate in vivo, using the rat eye via intravitreal injection, resulted in sequence specific mRNA knockdown in the retina with no obvious signs of toxicity, as judged by ophthalmic examination.

Show MeSH

Related in: MedlinePlus

Molecular dynamic simulationof conjugate 1b. Simulationdetails and additional graphical representations can be found in the Supporting Information.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4334295&req=5

fig6: Molecular dynamic simulationof conjugate 1b. Simulationdetails and additional graphical representations can be found in the Supporting Information.

Mentions: To date, molecular modeling on siRNA conjugateshas been limited.Furthermore, conjugates 1b and 5 representthe first examples of molecular umbrella–siRNA conjugates.Thus, we saw this as an opportunity to gain insight into the interactionsbetween the umbrella, siRNA, and an aqueous environment. To betterunderstand the intramolecular interactions, classical molecular dynamics(MD) simulations were performed. The AMBER force field was selectedfor approximating the atomic interactions.14 This force field is particularly appropriate for modeling interactionsbetween nucleic acids and small molecules especially where covalentbonds are involved.15 For this hybrid systemwe also employed the AM1 bond charge corrected version for which wehave extensive experience and confidence.16 Sodium chloride (NaCl) was added at a physiciological concentrationof 150 mM. In addition sodium ions (Na+) were added toensure charge neutrality. The initial conformation of the double strandnucleic acids was placed in the A-form, while the umbrella assumeda more extended form to minimize any preference for the intramolecularumbrella–siRNA interaction. This initial configuration of theumbrella–siRNA conjugate, explicit water, and ions was minimizedbefore slowly heating to ∼310 K. After reaching constant pressureequilibrium, a 40 ns MD simulation was performed using a 0.001 pstime step. Figure 6 shows a snapshot of thefinal conformation of the conjugate resulting from these calculations.As predicted, the hydrophobic faces of six of the cholic acids condenseupon themselves and the hydroxyl moieties interact with the aqueousenvironment. Encouragingly, two of the cholic acid hydrophobic facesinteract with the hydrophobic wedge of the siRNA, lending supportto the amphiphilic nature of the umbrella conjugate.


Molecular umbrella conjugate for the ocular delivery of siRNA.

Janout V, Cline LL, Feuston BP, Klein L, O'Brien A, Tucker T, Yuan Y, O'Neill-Davis LA, Peiffer RL, Nerurkar SS, Jadhav V, Tellers DM, Regen SL - Bioconjug. Chem. (2014)

Molecular dynamic simulationof conjugate 1b. Simulationdetails and additional graphical representations can be found in the Supporting Information.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4334295&req=5

fig6: Molecular dynamic simulationof conjugate 1b. Simulationdetails and additional graphical representations can be found in the Supporting Information.
Mentions: To date, molecular modeling on siRNA conjugateshas been limited.Furthermore, conjugates 1b and 5 representthe first examples of molecular umbrella–siRNA conjugates.Thus, we saw this as an opportunity to gain insight into the interactionsbetween the umbrella, siRNA, and an aqueous environment. To betterunderstand the intramolecular interactions, classical molecular dynamics(MD) simulations were performed. The AMBER force field was selectedfor approximating the atomic interactions.14 This force field is particularly appropriate for modeling interactionsbetween nucleic acids and small molecules especially where covalentbonds are involved.15 For this hybrid systemwe also employed the AM1 bond charge corrected version for which wehave extensive experience and confidence.16 Sodium chloride (NaCl) was added at a physiciological concentrationof 150 mM. In addition sodium ions (Na+) were added toensure charge neutrality. The initial conformation of the double strandnucleic acids was placed in the A-form, while the umbrella assumeda more extended form to minimize any preference for the intramolecularumbrella–siRNA interaction. This initial configuration of theumbrella–siRNA conjugate, explicit water, and ions was minimizedbefore slowly heating to ∼310 K. After reaching constant pressureequilibrium, a 40 ns MD simulation was performed using a 0.001 pstime step. Figure 6 shows a snapshot of thefinal conformation of the conjugate resulting from these calculations.As predicted, the hydrophobic faces of six of the cholic acids condenseupon themselves and the hydroxyl moieties interact with the aqueousenvironment. Encouragingly, two of the cholic acid hydrophobic facesinteract with the hydrophobic wedge of the siRNA, lending supportto the amphiphilic nature of the umbrella conjugate.

Bottom Line: The synthesis, computer modeling, and biological activity of an octawalled molecular umbrella short interfacing RNA (siRNA) conjugate is described.This molecular umbrella-siRNA conjugate exhibited mRNA knockdown activity in vitro in the absence of a transfection reagent.Evaluation of this molecular umbrella conjugate in vivo, using the rat eye via intravitreal injection, resulted in sequence specific mRNA knockdown in the retina with no obvious signs of toxicity, as judged by ophthalmic examination.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Lehigh University , Bethlehem, Pennsylvania 18015, United States.

ABSTRACT
The synthesis, computer modeling, and biological activity of an octawalled molecular umbrella short interfacing RNA (siRNA) conjugate is described. This molecular umbrella-siRNA conjugate exhibited mRNA knockdown activity in vitro in the absence of a transfection reagent. Evaluation of this molecular umbrella conjugate in vivo, using the rat eye via intravitreal injection, resulted in sequence specific mRNA knockdown in the retina with no obvious signs of toxicity, as judged by ophthalmic examination.

Show MeSH
Related in: MedlinePlus