1
|
Yuan L, Liang X, He L. Unveiling dissociation mechanisms and binding patterns in the UHRF1-DPPA3 complex via multi-replica molecular dynamics simulations. J Mol Model 2024; 30:173. [PMID: 38767734 DOI: 10.1007/s00894-024-05946-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/16/2024] [Indexed: 05/22/2024]
Abstract
CONTEXT Ubiquitin-like with PHD and RING finger domain containing protein 1 (UHRF1) is responsible for preserving the stability of genomic methylation through the recruitment of DNA methyltransferase 1 (DNMT1). However, the interaction between Developmental pluripotency associated 3 (DPPA3) and the pre-PHD-PHD (PPHD) domain of UHRF1 hinders the nuclear localization of UHRF1. This disruption has implications for potential cancer treatment strategies. Drugs that mimic the binding pattern between DPPA3 and PPHD could offer a promising approach to cancer treatment. Our study reveals that DPPA3 undergoes dissociation from the C-terminal through three different modes of helix unfolding. Furthermore, we have identified key residue pairs involved in this dissociation process and potential drug-targeting residues. These findings offer valuable insights into the dissociation mechanism of DPPA3 from PPHD and have the potential to inform the design of novel drugs targeting UHRF1 for cancer therapy. METHODS To comprehend the dissociation process and binding patterns of PPHD-DPPA3, we employed enhanced sampling techniques, including steered molecular dynamics (SMD) and conventional molecular dynamics (cMD). Additionally, we utilized self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. The Gromacs software was used for performing molecular dynamics simulations, and the AMBER FF14SB force field was applied to the protein.
Collapse
Affiliation(s)
- Longxiao Yuan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300353, China
| | - Xiaodan Liang
- School of Computer Sciences and Technology, Tiangong University, Tianjin, 300387, China.
| | - Lei He
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| |
Collapse
|
2
|
Yuan L, Liang X, He L. Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex. ACS OMEGA 2024; 9:20819-20831. [PMID: 38764655 PMCID: PMC11097150 DOI: 10.1021/acsomega.3c09433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/27/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage repair responses. For this process to occur, it is necessary for PHF8 to dissociate from Topbp1. Topbp1 binds to the acidic patch sequence (APS) of PHF8 through its C-terminal BRCT7/8 domain, and disrupting this interaction could be a promising strategy for cancer treatment. To investigate the dissociation process and binding pattern of BRCT7/8-PHF8, we employed enhanced sampling techniques, such as steered molecular dynamics (SMD) simulations and accelerated molecular dynamics (aMD) simulations, along with self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. Our results demonstrate that the dissociation of PHF8 from BRCT7/8 starts from the N-terminus, leading to the unfolding of the N-terminal helix. Additionally, we identified critical residues that play a pivotal role in this dissociation process. These findings provide valuable insights into the disassociation of PHF8 from BRCT7/8, which could potentially guide the development of novel drugs targeting Topbp1 for cancer therapy.
Collapse
Affiliation(s)
- Longxiao Yuan
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Xiaodan Liang
- School
of Computer Sciences and Technology, Tiangong
University, Tianjin 300387, China
| | - Lei He
- Institute
for Fetology, The First Affiliated Hospital
of Soochow University, Suzhou 215006, China
| |
Collapse
|
3
|
Frigerio G, Donadoni E, Siani P, Vertemara J, Motta S, Bonati L, Gioia LD, Valentin CD. Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α Vβ 3 by atomistic molecular dynamics and machine learning. NANOSCALE 2024; 16:4063-4081. [PMID: 38334981 DOI: 10.1039/d3nr05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Active targeting strategies have been proposed to enhance the selective uptake of nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the effectiveness of this approach. However, no mechanistic studies have yet revealed the atomistic details of the interactions between ligand-activated NPs and integrins. As a case study, here we investigate, by means of advanced molecular dynamics simulations (MD) and machine learning methods (namely equilibrium MD, binding free energy calculations and training of self-organized maps), the interaction of a cyclic-RGD-conjugated PEGylated TiO2 NP (the nanodevice) with the extracellular segment of integrin αVβ3 (the target), the latter experimentally well-known to be over-expressed in several solid tumors. Firstly, we proved that the cyclic-RGD ligand binding to the integrin pocket is established and kept stable even in the presence of the cumbersome realistic model of the nanodevice. In this respect, the unsupervised machine learning analysis allowed a detailed comparison of the ligand/integrin binding in the presence and in the absence of the nanodevice, which unveiled differences in the chemical features. Then, we discovered that unbound cyclic RGDs conjugated to the NP largely contribute to the interactions between the nanodevice and the integrin. Finally, by increasing the density of cyclic RGDs on the PEGylated TiO2 NP, we observed a proportional enhancement of the nanodevice/target binding. All these findings can be exploited to achieve an improved targeting selectivity and cellular uptake, and thus a more successful clinical outcome.
Collapse
Affiliation(s)
- Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Luca De Gioia
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, Italy
| |
Collapse
|
4
|
Donadoni E, Frigerio G, Siani P, Motta S, Vertemara J, De Gioia L, Bonati L, Di Valentin C. Molecular Dynamics for the Optimal Design of Functionalized Nanodevices to Target Folate Receptors on Tumor Cells. ACS Biomater Sci Eng 2023; 9:6123-6137. [PMID: 37831005 PMCID: PMC10646887 DOI: 10.1021/acsbiomaterials.3c00942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
Atomistic details on the mechanism of targeting activity by biomedical nanodevices of specific receptors are still scarce in the literature, where mostly ligand/receptor pairs are modeled. Here, we use atomistic molecular dynamics (MD) simulations, free energy calculations, and machine learning approaches on the case study of spherical TiO2 nanoparticles (NPs) functionalized with folic acid (FA) as the targeting ligand of the folate receptor (FR). We consider different FA densities on the surface and different anchoring approaches, i.e., direct covalent bonding of FA γ-carboxylate or through polyethylene glycol spacers. By molecular docking, we first identify the lowest energy conformation of one FA inside the FR binding pocket from the X-ray crystal structure, which becomes the starting point of classical MD simulations in a realistic physiological environment. We estimate the binding free energy to be compared with the existing experimental data. Then, we increase complexity and go from the isolated FA to a nanosystem decorated with several FAs. Within the simulation time framework, we confirm the stability of the ligand-receptor interaction, even in the presence of the NP (with or without a spacer), and no significant modification of the protein secondary structure is observed. Our study highlights the crucial role played by the spacer, FA protonation state, and density, which are parameters that can be controlled during the nanodevice preparation step.
Collapse
Affiliation(s)
- Edoardo Donadoni
- Dipartimento
di Scienza dei Materiali, Università
di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Giulia Frigerio
- Dipartimento
di Scienza dei Materiali, Università
di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Paulo Siani
- Dipartimento
di Scienza dei Materiali, Università
di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Stefano Motta
- Dipartimento
di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Jacopo Vertemara
- Dipartimento
di Biotecnologie e Bioscienze, Università
di Milano-Bicocca, Piazza
della Scienza 1, 20126 Milano, Italy
| | - Luca De Gioia
- Dipartimento
di Biotecnologie e Bioscienze, Università
di Milano-Bicocca, Piazza
della Scienza 1, 20126 Milano, Italy
| | - Laura Bonati
- Dipartimento
di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Cristiana Di Valentin
- Dipartimento
di Scienza dei Materiali, Università
di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
- BioNanoMedicine
Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, 20854 Vedano al Lambro, Italy
| |
Collapse
|
5
|
Motta S, Siani P, Donadoni E, Frigerio G, Bonati L, Di Valentin C. Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles. NANOSCALE 2023; 15:7909-7919. [PMID: 37066796 DOI: 10.1039/d3nr00397c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Inorganic nanoparticles show promising properties that allow them to be efficiently used as drug carriers. The main limitation in this type of application is currently the drug loading capacity, which can be overcome with a proper functionalization of the nanoparticle surface. In this study, we present, for the first time, a computational approach based on metadynamics to estimate the binding free energy of the doxorubicin drug (DOX) to a functionalized TiO2 nanoparticle under different pH conditions. On a thermodynamic basis, we demonstrate the robustness of our approach to capture the overall mechanism behind the pH-triggered release of DOX due to environmental pH changes. Notably, binding free energy estimations align well with what is expected for a pH-sensitive drug delivery system. Based on our results, we envision the use of metadynamics as a promising computational tool for the rational design and in silico optimization of organic ligands with improved drug carrier properties.
Collapse
Affiliation(s)
- Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy
| |
Collapse
|
6
|
Stevens AO, Kazan IC, Ozkan B, He Y. Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations. Protein Sci 2022; 31:e4474. [PMID: 36251217 PMCID: PMC9667829 DOI: 10.1002/pro.4474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
The PDZ family is comprised of small modular domains that play critical roles in the allosteric modulation of many cellular signaling processes by binding to the C-terminal tail of different proteins. As dominant modular proteins that interact with a diverse set of peptides, it is of particular interest to explore how different binding partners induce different allosteric effects on the same PDZ domain. Because the PICK1 PDZ domain can bind different types of ligands, it is an ideal test case to answer this question and explore the network of interactions that give rise to dynamic allostery. Here, we use all-atom molecular dynamics simulations to explore dynamic allostery in the PICK1 PDZ domain by modeling two PICK1 PDZ systems: PICK1 PDZ-DAT and PICK1 PDZ-GluR2. Our results suggest that ligand binding to the PICK1 PDZ domain induces dynamic allostery at the αA helix that is similar to what has been observed in other PDZ domains. We found that the PICK1 PDZ-ligand distance is directly correlated with both dynamic changes of the αA helix and the distance between the αA helix and βB strand. Furthermore, our work identifies a hydrophobic core between DAT/GluR2 and I35 as a key interaction in inducing such dynamic allostery. Finally, the unique interaction patterns between different binding partners and the PICK1 PDZ domain can induce unique dynamic changes to the PICK1 PDZ domain. We suspect that unique allosteric coupling patterns with different ligands may play a critical role in how PICK1 performs its biological functions in various signaling networks.
Collapse
Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
| | - I. Can Kazan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Banu Ozkan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Yi He
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
| |
Collapse
|
7
|
Hendrix E, Motta S, Gahl RF, He Y. Insight into the Initial Stages of the Folding Process in Onconase Revealed by UNRES. J Phys Chem B 2022; 126:7934-7942. [PMID: 36179061 DOI: 10.1021/acs.jpcb.2c04770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unfolded state of proteins presents many challenges to elucidate the structural basis for biological function. This state is characterized by a large degree of structural heterogeneity which makes it difficult to generate structural models. However, recent experiments into the initial folding events of the 104-residue ribonuclease homologue onconase (ONC) were able to identify the regions in the protein that participate in the initial folding of this protein. Therefore, to gain additional structural insight into the unfolded state of proteins, this study utilized molecular dynamics simulations using the UNited-RESidue (UNRES) force field to evaluate whether there is a good agreement between the experimentally determined initial structures and the structures identified by computer simulations along a folding pathway. Indeed, these UNRES simulations accurately identified the two regions experimentally observed to form the initial native structure along the folding pathway of ONC. In addition, these regions are determined to be chain folding initiation sites (CFIS) according to methods developed previously. Subsequent self-organization maps (SOM) analysis has revealed key structural states involved in these early folding events.
Collapse
Affiliation(s)
- Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan20126, Italy
| | - Robert F Gahl
- Division of Extramural Activities, National Cancer Institute, National Institutes of Health, Bethesda, Maryland20850, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico87131, United States
| |
Collapse
|