---
title: "Surface Chemistry and pH Control Structural Dynamics and Drug Binding in PETIM and PAMAM Dendrimers"
id: "biorxiv-18-surface-functionality-and-ph-govern-structural-dynamics-and-drug-binding-in"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-18-surface-functionality-and-ph-govern-structural-dynamics-and-drug-binding-in"
content_type: "clinical_feed_article"
specialty: "Pharmacology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1?rss=1"
published_at: "2026-08-07T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Surface Chemistry and pH Control Structural Dynamics and Drug Binding in PETIM and PAMAM Dendrimers
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-18-surface-functionality-and-ph-govern-structural-dynamics-and-drug-binding-in
- **Specialty:** [Pharmacology](https://medichelpline.com/clinical-feed/pharmacology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1?rss=1)
- **Published At:** 2026-08-07T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- This preprint reports all-atom molecular dynamics simulations of **PETIM** and **PAMAM** dendrimers (five generations each) with different core types (O-core, N-core), surface functional groups (amine, carboxylic acid, sugar) and protonation states. - Protonation of tertiary branch-point amines expands dendrimer architecture, increases internal porosity and hydration, and amplifies structural fluctuations across both dendrimer families. - Non-protonated amine (-NH2, NP), carboxylic acid (-COOH, NP), and deprotonated carboxylate (-COO-, DeP) terminal groups favor more compact conformations with lower structural dynamics. - Sugar-terminated dendrimers (β-galactose PETIM; D-glucose PAMAM) are the most hydrated and the most structurally rigid among the tested surface chemistries. - Amine-terminated dendrimers display the largest conformational mobility compared with sugar- and carboxylate-terminated systems. - Overall hydration differs by family: **PAMAM** dendrimers with -NH2, -NH3+, and -COO- terminals are generally more hydrated than equivalent **PETIM** systems, but β-galactose-terminated PETIMs are more hydrophilic than D-glucose-terminated PAMAMs. - N-core PETIM dendrimers adopt more compact and spherical shapes than corresponding O-core PETIM dendrimers. - Drug-binding simulations indicate that **curcumin** complexation is dominated by van der Waals interactions, while **doxorubicin** binding is driven primarily by electrostatic interactions. - Surface terminations -NH2 (NP), -NH3+ (P), -COOH (NP), and -COO- (DeP) show the most favorable drug-binding characteristics in the simulated systems. - Except for deprotonated carboxylate systems, curcumin exhibits stronger binding than doxorubicin in these simulations. - The study links surface functionality, protonation state, dendrimer architecture, and drug-binding behavior, offering molecular-level design principles for pH-responsive dendrimer nanocarriers aimed at improved drug loading and controlled release. - This work is a preprint and has not been peer reviewed; supplementary materials are available but specific methodological parameters and numerical results beyond the summary were not reported in the abstract.
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Anuj Garg 1 Sri Sathya Sai Institute of Higher Learning (SSSIHL), Puttaparthi, Andhra Pradesh; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Anuj%2BGarg%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Garg%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAnuj%2BGarg%2B) * [ORCID record for Anuj Garg](http://orcid.org/0000-0003-3968-3884 "Open in new tab") Santosh Mogurampelly 2 Indian Institute of Technology Jodhpur, Rajasthan * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Santosh%2BMogurampelly%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Mogurampelly%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASantosh%2BMogurampelly%2B) * [ORCID record for Santosh Mogurampelly](http://orcid.org/0000-0002-3145-4377 "Open in new tab") Subbarao Kanchi 1 Sri Sathya Sai Institute of Higher Learning (SSSIHL), Puttaparthi, Andhra Pradesh; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Subbarao%2BKanchi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kanchi%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASubbarao%2BKanchi%2B) * [ORCID record for Subbarao Kanchi](http://orcid.org/0000-0001-9147-0101 "Open in new tab") * For correspondence: subbaraokanchi@sssihl.edu.in * [Abstract](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5688696/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5688696/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5688696/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5688696/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5688696/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Surface functionality and pH play a decisive role in governing the structural dynamics, hydration, and drug-binding behaviour of dendrimers. Here, all-atom molecular dynamics (MD) simulations were performed on five generations of PAMAM (G1-G5) and PETIM (G2-G6) dendrimers with O-core and N-core architectures, functionalized with amine, carboxylic acid, or sugar terminal groups under different protonation states. Protonation of the tertiary branch-point amines expands the dendrimer structure, increases internal porosity and hydration, and enhances structural fluctuations across both families. In contrast, non-protonated amine -NH2 (NP) and carboxylic acid -COOH (NP) terminated dendrimers, together with deprotonated carboxylate-COO- (DeP) systems, retain comparatively compact conformations. Sugar-functionalized dendrimers (β-galactose-terminated PETIM and D-glucose-terminated PAMAM) are most hydrated and structurally rigid, whereas amine-terminated dendrimers exhibit the greatest conformational dynamics. PAMAM dendrimers with -NH2, -NH3+, and -COO- terminal groups are generally more hydrated than their PETIM counterparts. However, β-galactose-terminated PETIM dendrimers aremore hydrophilic than D-glucose-terminated PAMAM dendrimers. N-core PETIM dendrimers also adopt more compact and spherical conformations than equivalent O-core PETIM dendrimers. Drug-binding MD simulations show that curcumin binding is dominated by van der Waals (vdW) interactions, whereas doxorubicin complexation is primarily driven by electrostatic interactions. Among the investigated surface functionalities, -NH2 (NP), -NH3+ (P), -COOH (NP), and -COO-(DeP) terminations exhibit the most favourable drug-binding characteristics. Except for deprotonated carboxylate systems, curcumin binds more strongly than doxorubicin. Overall, these findingsestablish molecular-level relationships between surface functionality, protonation state, dendrimer architecture, and drug-binding behaviour, providing design principles for pH-responsive dendrimer nanocarriers with enhanced drug-loading and controlled-release performance. ### Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC-ND 4.0 International license](http://creativecommons.org/licenses/by-nc-nd/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/08/07/2026.08.04.742721.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.08.04.742721v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Surface Functionality and pH Govern Structural Dynamics and Drug Binding in PETIM and PAMAM Dendrimers Anuj Garg, Santosh Mogurampelly, Subbarao Kanchi bioRxiv 2026.08.04.742721; doi: https://doi.org/10.64898/2026.08.04.742721 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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