2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
January 22nd, 2025
Version: 1
Indian Institute of Science
biophysics
biorxiv

siRNA complexation with Galactose-Functionalized Dendrimer: PAMAM vs PETIM

Maity, T.Open in Google Scholar•Kumar, Y.Open in Google Scholar•Maiti, P. K.Open in Google Scholar

siRNA-based therapies hold promise for treating various diseases, but efficient and targeted delivery remains challenging. This study explored the potential of galactose-functionalized poly(amidoamine) (Gal-PAMAM) and poly(propyl ether amine) (Gal-PETIM) dendrimers as siRNA carriers using all-atom molecular dynamics simulations. This study revealed distinct complexation behavior for both the system in physiological (pH [~] 7) and high (pH [~] 10) environments. Electrostatic interactions dominated complexation, with PMF profiles revealing stronger binding affinity for Gal-PAMAM/siRNA at pH 7. siRNA displayed lower flexibility at pH 7 for both complexes, indicating enhanced stability. These findings suggest that Gal-PAMAM dendrimers at physiological pH hold promise for efficient siRNA delivery due to their superior complex stability and interaction strength. However, in polar solvents, Gal-PETIM exhibits hydrophobic behavior, enabling rapid delivery.

Similar Papers

biorxiv
Thu May 08 2025
Topology, Kinetics and Inheritance in Clonal Colonies of Bone Marrow Stromal Cells
Bone marrow stromal cells (BMSCs), whose populations contain multipotent skeletal stem cells with relevant therapeutic applications, are known to produce very heterogeneous colonies upon in vitro culture, a trait that may severely hinder the clinical usefulness of BMSC-based therapies. Therefore, reaching a better insight on the nature of such heterogeneity, as well as on the factors determining i...
Allegrezza, A.
•
Beschi, R.
•
Caudo, D.
•
Cavagna, A.
...•
Rotondi, F. S.
biorxiv
Thu May 08 2025
Atomic Conformational Dynamics and Actin-Crosslinking Function of Alpha-Actinin Revealed by SimHS-AFMfit
Alpha-actinin is a crucial actin-binding protein involved in cellular functions like muscle contractility, mechanosensation, and cell division. Studying its atomic structure and dynamics is challenging due to protein complexity and imaging limitations. To address this, we developed SimHS-AFMfit, integrating high-speed AFM (HS-AFM), AFMfit (a flexible fitting technique), and molecular dynamics (MD)...
Ngo, K. X.
•
Sumikama, T.
•
Vuillemot, R.
•
Nguyen, H. G.
...•
Grudinin, S.
biorxiv
Thu May 08 2025
A Toolbox for the Personalization of Plasmonic Photothermal Therapy in Orthotopic Mouse Tumor Models
The clinical translation of plasmonic photothermal therapy is hindered by a lack of reliable personalization protocols. In this study we implemented a non-invasive toolbox to assess how tumor optical and hemodynamic properties can serve as markers of progression and be used in personalized simulations to extrapolate therapy conditions, both necessary steps for individualized treatment planning. Th...
Fernandez Esteberena, P. R.
•
Vilches, C.
•
Morales-Dalmau, J.
•
Mireles, M.
...•
Durduran, T.
biorxiv
Thu May 08 2025
Unifying Orientation-Dependent Relaxation and Diffusion Around Axonal Fibers from DTI: Characterizing Fiber-Tract-Specific Anisotropic R2 Profiles of the Corpus Callosum
This work aims to characterize fiber-tract-specific orientation-dependent R2 from the seven callosal segments (CC1-CC7) based on human brain Connectome high-resolution DTI datasets. WM voxels from each segment were masked by the thresholds of FA and mode of anisotropy. Encoded in T2W images (b-value = 0), an orientation-dependent R2 profile was constructed based on voxel-wise fiber orientations an...
Pang, Y.
•
Raja, R.
•
Reddick, W. E.
biorxiv
Thu May 08 2025
MICLEAR: Intelligent Molecular Cytology for Intraoperative Margin Assessment of Pancreatic Ductal Adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is a highly mortal cancer whose only potentially curative treatment is surgical resection. Intraoperative assessment of its surgical margins is vital for patient survival. Frozen-section biopsy is routinely performed for this purpose. However, its high dependence on pathologists' experience frequently poses diagnostic discrepancies. The essential invasivenes...
Fang, T.
•
Liu, D.
•
Chen, X.
•
Zhou, K.
...•
Yue, S.
biorxiv
Thu May 08 2025
Simulated Solute Tempering 2
Molecular dynamics (MD) simulations are powerful tools for studying the movement and interactions of molecules, but they can be computationally expensive, especially for large biomolecules like proteins. This is problematic because accurately simulating the motions of these molecules is key to understanding their function. Enhanced sampling methods, such as Simulated Tempering (ST), temperature Re...
Stratmann, D.
•
Moroy, G.
•
Tuffery, P.
•
Murail, S.
biorxiv
Thu May 08 2025
gorder: Comprehensive tool for calculating lipid orderparameters from molecular simulations
Lipid order parameters are an important metric for quantifying the molecular structure of biological membranes. They can be derived from both molecular simulations and experimental measurements, enabling robust comparisons between the two. Although methods for calculating lipid order parameters from molecular dynamics simulations of membrane systems at various resolutions are well established, a c...
Bartos, L.
•
Pajtinka, P.
•
Vacha, R.
biorxiv
Thu May 08 2025
Delayed Extracellular Matrix Negative Feedback Contributes to Nascent Adhesion Dynamics: Mathematical Modeling and Analysis
Cell migration, both in vivo and in vitro, is a complex process governed by mechano-chemical interactions between cells and the extracellular matrix (ECM). These interactions, mediated by cell membrane receptors called integrins, involve bidirectional signaling between the intracellular actin cytoskeleton and the ECM. Integrins bind with cytoplasmic proteins to form adhesion complexes of varying s...
Andasari, V.
•
Syafiie, S.
biorxiv
Thu May 08 2025
Structural basis of PPARγ-mediated transcriptional repression by the covalent inverse agonist FX-909
Hyperactivation of peroxisome proliferator-activated receptor gamma (PPAR{gamma})-mediated transcription promotes tumor growth in urothelial (bladder) cancer, which can be inhibited by pharmacological compounds that repress PPAR{gamma} activity. FX-909 is a covalent PPAR{gamma} inverse agonist currently in phase 1 clinical trials for advanced solid malignancies including muscle-invasive bladder ca...
Laughlin, Z. T.
•
Arifova, L.
•
Munoz-Tello, P.
•
Yu, X.
...•
Kojetin, D. J.
biorxiv
Wed May 07 2025
Millisecond bidirectional protein translocation by a AAA+ disaggregation machine
How biological machines utilize ATP to facilitate mechanical work remains heavily contested. ClpB is a quality control machine of the AAA+ family that salvages misfolded and aggregated proteins by forcibly translocating them through its lumen. Structural studies of this and similar machines have suggested a power-stroke translocation mechanism directly coupled to sequential subunit motion. However...
Casier, R.
•
Levy, D.
•
Riven, I.
•
Barak, Y.
•
Haran, G.