1
|
Pacak P, Kluger C, Vogel V. Molecular dynamics of JUNO-IZUMO1 complexation suggests biologically relevant mechanisms in fertilization. Sci Rep 2023; 13:20342. [PMID: 37990051 PMCID: PMC10663542 DOI: 10.1038/s41598-023-46835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
JUNO-IZUMO1 binding is the first known physical link created between the sperm and egg membranes in fertilization, however, how this initiates sperm-egg fusion remains elusive. As advanced structural insights will help to combat the infertility crisis, or advance fertility control, we employed all-atom Molecular Dynamics (MD) to derive dynamic structural insights that are difficult to obtain experimentally. We found that the hydrated JUNO-IZUMO1 interface is composed of a large set of short-lived non-covalent interactions. The contact interface is destabilized by strategically located point mutations, as well as by Zn2+ ions, which shift IZUMO1 into the non-binding "boomerang" conformation. We hypothesize that the latter might explain how the transient zinc spark, as released after sperm entry into the oocyte, might contribute to block polyspermy. To address a second mystery, we performed another set of simulations, as it was previously suggested that JUNO in solution is unable to bind to folate despite it belonging to the folate receptor family. MD now suggests that JUNO complexation with IZUMO1 opens up the binding pocket thereby enabling folate insertion. Our MD simulations thus provide crucial new hypotheses how the dynamics of the JUNO-IZUMO1 complex upon solvation might regulate fertility.
Collapse
Affiliation(s)
- Paulina Pacak
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Carleen Kluger
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität, München, Munich, Germany
- Evotec München GmbH, Neuried, Germany
| | - Viola Vogel
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
2
|
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
|
3
|
Kordzadeh A, Zarif M, Amjad-Iranagh S. Molecular dynamics insight of interaction between the functionalized-carbon nanotube and cancerous cell membrane in doxorubicin delivery. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 230:107332. [PMID: 36603233 DOI: 10.1016/j.cmpb.2022.107332] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/08/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND OBJECTIVE Doxorubicin (DOX) is a known anticancer drug which is widely used in cancer therapy. Carbon nanotubes (CNTs) are among the most promising platforms for smart drug delivery applications. However, due to the toxicity and their low sulubility their application is limited and their functionalization with wide range of biomolecules are suggested. Therefore, the functionalized carbon nanotubes (f-CNT) with carboxyl (CNT-COO) and folic acid (CNT-COO-FA) were investigated as drug-carrier. METHODS Molecular dynamics (MD) simulation along with the Density Functional Theory (DFT) methods are being used to study the drug loading process on functionalized carbon nanotubes. RESULTS The results indicate that doxorubicin molecules interact more with CNT-COO-FA than CNT-COO. The embedded dipalmitoylphosphatidylcholine (DPPC) lipid bilayer with a folate receptor was considered a cancerous cell's representative model. Then the drug release from the f-CNTs near the lipid bilayer was simulated. The results showed that CNT-COO-FA with a pH and ligand-sensitive mechanism strongly interacts with cancerous cells, which led to higher drug release, in agreement with the experimental results. The conformational changes of the lipid bilayer and folate receptor during drug release were evaluated. The analysis showed that drug release from CNT-COO-FA has significantly changed lipid bilayer and receptor conformations. The obtained results were interpreted and justified by considering the molecular mechanisms which control the drug delivery in the studied systems. CONCLUSIONS Based on the obtained results, CNT-COO-FA has a better performance during the drug release compared to CNT-COO in delivering doxorubicin. Both pH and ligand sensitive mechanisms are found to be responsible for higher drug delivery efficiency of CNT-COO-FA. In contrast, CNT-COO can only enhance drug delivery efficiently with a pH-sensitive mechanism.
Collapse
Affiliation(s)
- Azadeh Kordzadeh
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tehran 145888-9694, Tehran, Iran
| | - Mahdi Zarif
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 19839-9411, Tehran, Iran.
| | - Sepideh Amjad-Iranagh
- Department of Materials and Metallurgical Engineering, Amirkabir University of Technology, Tehran 115875-4313, Tehran, Iran.
| |
Collapse
|
4
|
Schaber EN, Ivanova N, Iliev S, Petrova J, Gocheva G, Madjarova G, Ivanova A. Initial Stages of Spontaneous Binding of Folate-Based Vectors to Folate Receptor-α Observed by Unbiased Molecular Dynamics. J Phys Chem B 2021; 125:7598-7612. [PMID: 34247488 DOI: 10.1021/acs.jpcb.1c00488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Active targeting is a prospective strategy for controlled drug delivery to malignant tumor tissues. One of the approaches relies on recognition of a bioactive ligand by a receptor expressed abundantly on the surface of cancer cell membranes. A promising ligand-receptor pair is folic acid (or its dianionic form, folate) combined with the folate receptor-α (FRα). A number of targeting drug delivery systems based on folate have been suggested, but the mechanism of binding of the ligand or its derivatives to the receptor is not fully known at the molecular level. The current study summarizes the results from unbiased all-atom molecular dynamics simulations at physiological conditions describing the binding of two forms of folate and four of its synthetically available derivatives to FRα. The models (ca. 185,000 atoms) contain one receptor molecule, embedded in the outer leaflet of a lipid bilayer, and one ligand, all immersed in saline. The bilayer represents a human cancer cell membrane and consists of 370 asymmetrically distributed lipid molecules from 35 types. The ability of the vector molecules to bind to the receptor, the position of binding, and the interactions between them are analyzed. Spontaneous binding on the nanosecond scale is observed for all molecules, but its time, position, and persistence depend strongly on the ligand. Only folate, 5-methyltetrahydrofolate, and raltitrexed bind selectively at the active site of the receptor. Two binding poses are observed, one of them (realized by raltitrexed) corresponding qualitatively to that reported for the crystallographic structure of the complex folate-FRα. Pemetrexed adsorbs nonspecifically on the protein surface, while methotrexate and pteroyl ornithine couple much less to the receptor. The molecular simulations reproduce qualitatively correctly the relative binding affinity measured experimentally for five of the ligands. Analysis of the interactions between the ligands and FRα shows that in order to accomplish specific binding to the active site, a combination of hydrogen bonding, π-stacking, and van der Waals and Coulomb attraction should be feasible simultaneously for the vector molecule. The reported results demonstrate that it is possible to observe receptor-ligand binding without applying bias by representing the local environment as close as possible and contain important molecular-level guidelines for the design of folate-based systems for targeted delivery of anticancer drugs.
Collapse
Affiliation(s)
- Ethan N Schaber
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Nikoleta Ivanova
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Stoyan Iliev
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Jasmina Petrova
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Gergana Gocheva
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Galia Madjarova
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| | - Anela Ivanova
- Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria
| |
Collapse
|
5
|
Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight. Molecules 2021; 26:molecules26041079. [PMID: 33670773 PMCID: PMC7922218 DOI: 10.3390/molecules26041079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
Collapse
|
6
|
Marashiyan M, Kalhor H, Ganji M, Rahimi H. Effects of tosyl-l-arginine methyl ester (TAME) on the APC/c subunits: An in silico investigation for inhibiting cell cycle. J Mol Graph Model 2020; 97:107563. [PMID: 32066079 DOI: 10.1016/j.jmgm.2020.107563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/11/2020] [Accepted: 02/01/2020] [Indexed: 11/28/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/c) is requisite for controlling mitosis, which is activated by Cdh1 and Cdc20 activators. Dysregulation of APC/c is observed in many cancers and is known as a targeted drug particularly in cancer drug resistance. It was shown that tosyl-l-arginine methyl ester (TAME), via mimicking isoleucine-arginine (IR) tail of co-activators, inhibits APC/c functions. However, structure details and interaction of TAME with APC/c are poorly defined. In the current study, a well-established set of computational methods was used to identify the best binding pocket in order to inhibit APC activity. Therefore, the interaction of IR tail and Cbox of co-activators, as well as TAME as an inhibitor, as an inhibitor, with APC3 and APC8 subunits of APC/c were analyzed, regarding structure, molecular docking, molecular dynamics, and free binding energy. The results indicated that TAME bound to APC3 with a higher binding affinity (∼-7.3 kcal/mol) than APC8 (∼-5.7 kcal/mol). Also, the binding free energy value obtained for the APC3-TAME was -22.25 ± 1.12 kcal/mol. According to binding free energies, van der Waals energy was the major favorable contributor to the ligand binding. These results offer that TAME had more affinity to interact with the APC3 subunit, at the IR binding pocket than the APC8 subunit at the Cbox binding pocket. In conclusion, IR binding pocket can serve as an appropriate potential target for TAME as an inhibitor of APC/c.
Collapse
Affiliation(s)
- Mahya Marashiyan
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hourieh Kalhor
- Cellular and Molecular Research Center,Qom University of Medical Sciences, Qom, Iran
| | - Maziar Ganji
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamzeh Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
7
|
Gocheva G, Ivanova N, Iliev S, Petrova J, Madjarova G, Ivanova A. Characteristics of a Folate Receptor-α Anchored into a Multilipid Bilayer Obtained from Atomistic Molecular Dynamics Simulations. J Chem Theory Comput 2019; 16:749-764. [PMID: 31639310 DOI: 10.1021/acs.jctc.9b00872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thorough computational description of the properties of membrane-anchored protein receptors, which are important for example in the context of active targeting drug delivery, may be achieved by models representing as close as possible the immediate environment of these macromolecules. An all-atom bilayer, including 35 different lipid types asymmetrically distributed among the two monolayers, is suggested as a model neoplastic cell membrane. One molecule of folate receptor-α (FRα) is anchored into its outer leaflet, and the behavior of the system is explored by atomistic molecular dynamics simulations. The total number of atoms in the model is ∼185 000. Three 1-μs-long simulations are carried out, where physiological conditions (310 K and 1 bar) are maintained with three different pressure scaling schemes. To evaluate the structure and the phase state of the membrane, the density profiles of the system, the average area per lipid, and the deuterium order parameter of the lipid tails are calculated. The bilayer is in liquid ordered state, and the specific arrangement varies between the three trajectories. The changes in the structure of FRα are investigated and are found time- and ensemble-dependent. The volume of the ligand binding pocket fluctuates with time, but this variation remains independent of the more global structural alterations. The latter are mostly "waving" motions of the protein, which periodically approaches and retreats from the membrane. The semi-isotropic pressure scaling perturbs the receptor most significantly, while the isotropic algorithm induces rather slow changes. Maintaining constant nonzero surface tension leads to behavior closest to the experimentally observed one.
Collapse
Affiliation(s)
- Gergana Gocheva
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Nikoleta Ivanova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Stoyan Iliev
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Jasmina Petrova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Galia Madjarova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Anela Ivanova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| |
Collapse
|
8
|
Metadynamics to Enhance Sampling in Biomolecular Simulations. Methods Mol Biol 2019. [PMID: 31396904 DOI: 10.1007/978-1-4939-9608-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.
Collapse
|
9
|
Gocheva G, Ivanova A. A Look at Receptor–Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. Mol Pharm 2019; 16:3293-3321. [DOI: 10.1021/acs.molpharmaceut.9b00250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gergana Gocheva
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| |
Collapse
|
10
|
Jiang Y, Wang C, Zhang M, Fei X, Gu Y. Interacted mechanism of functional groups in ligand targeted with folate receptor via docking, molecular dynamic and MM/PBSA. J Mol Graph Model 2018; 87:121-128. [PMID: 30537642 DOI: 10.1016/j.jmgm.2018.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/27/2022]
Abstract
Twenty novel compounds with different functional groups (-COOH, -OH, -NH2 and -CH3) were designed to study the interaction mechanism of ligands with folate receptors (FRs). The optimized structure and the dipole moment of the novel compounds were calculated by a density functional tight-binding method (DFTB). The binding mechanism of the compounds with FRs was studied by molecular docking, molecular dynamic (MD) simulations and MM/PBSA free energy calculations. The binding energies, root mean square displacement and root mean square fluctuation of the complexes were analyzed to further illustrate the effect of the functional groups. The functional groups play important roles in stabilizing the bound complexes. Compared to other groups, -OH is more stably linked with the compound. These data provide a theoretical basis for the design of novel compounds targeted with FRs.
Collapse
Affiliation(s)
- Yue Jiang
- School of Science, TianJin ChengJian University, Tianjin, China
| | - Cuihong Wang
- School of Science, TianJin ChengJian University, Tianjin, China.
| | - Meiling Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Xuening Fei
- School of Science, TianJin ChengJian University, Tianjin, China.
| | - Yingchun Gu
- School of Science, TianJin ChengJian University, Tianjin, China
| |
Collapse
|
11
|
Structural analysis of binding functionality of folic acid-PEG dendrimers against folate receptor. J Mol Graph Model 2017; 72:201-208. [PMID: 28110184 DOI: 10.1016/j.jmgm.2017.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/23/2016] [Accepted: 01/04/2017] [Indexed: 12/27/2022]
Abstract
Dendrimers functionalized with folic acid (FA) are drug delivery systems that can selectively target cancer cells with folate receptors (FR-α) overexpression. Incorporation of polyethylene glycol (PEG) can enhance dendrimers solubility and pharmacokinetics, but ligand-receptor binding must not be affected. In this work we characterized, at atomic level, the binding functionality of conventional site-specific dendrimers conjugated with FA with PEG 750 or PEG 3350 as a linker. After Molecular Dynamics simulation, we observed that both PEG's did not interfere over ligand-receptor binding functionality. Although binding kinetics could be notably affected, the folate fragment from both dendrimers remained exposed to the solvent before approaching selectively to FR-α. PEG 3350 provided better solubility and protection from enzymatic degradation to the dendrimer than PEG 750. Also, FA-PEG3350 dendrimer showed a slightly better interaction with FR-α than FA-PEG750 dendrimer. Therefore, theoretical evidence supports that both dendrimers are suitable as drug delivery systems for cancer therapies.
Collapse
|
12
|
Nutho B, Nunthaboot N, Wolschann P, Kungwan N, Rungrotmongkol T. Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes. RSC Adv 2017. [DOI: 10.1039/c7ra09387j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of various molecular dynamics methods enables the detailed investigation of association processes, like host–guest complexes, including their dynamics and, additionally, the release of the guest compound.
Collapse
Affiliation(s)
- Bodee Nutho
- Program in Biotechnology
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry
- Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150
| | - Peter Wolschann
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| | - Nawee Kungwan
- Department of Chemistry
- Faculty of Science
- Chiang Mai University
- Chiang Mai 50200
- Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| |
Collapse
|
13
|
Novel Water-Borne Polyurethane Nanomicelles for Cancer Chemotherapy: Higher Efficiency of Folate Receptors Than TRAIL Receptors in a Cancerous Balb/C Mouse Model. Pharm Res 2016; 33:1426-39. [PMID: 26908046 DOI: 10.1007/s11095-016-1884-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/16/2016] [Indexed: 01/17/2023]
Abstract
PURPOSE Since the introduction of nanocarriers, the delivery of chemotherapeutic agents for treatment of patients with cancer has been possible with better effectiveness. The latest findings are also support that further enhancement in therapeutic effectiveness of these nanocarriers can be attained, if surface decoration with proper targeting agents is considered. METHODS This study aimed at treating a variety of 4T1 murine breast cancer cell line, mainly demonstrating high folate and TRAIL receptor expression of cancerous cells. The therapeutic efficacy of paclitaxel loaded Cremophore EL (Taxol®), paclitaxel loaded waterborne polyurethane nanomicelles (PTX-PU) and paclitaxel loaded waterborne polyurethane nanomicelles conjugated with folate (PTX-PU-FA) and TRAIL (PTX-PU-TRAIL) on treating 4T1 cell was also compared. RESULTS The findings that worth noting are: PTX-PU outperformed Taxol® in a Balb/C mouse model, furthermore, tumor growth was adequately curbed by folate and TRAIL-decorated nanomicelles rather than the unconjugated formulation. Tumors of mice treated with PTX-PU-FA and PTX-PU-TRAIL shrank substantially compared to those treated with Taxol®, PTX-PU and PTX-PU-TRAIL (average 573 mm(3) versus 2640, 846, 717 mm(3) respectively), 45 days subsequent to tumor inoculation. The microscopic study of hematoxylin-eosin stained tumors tissue and apoptotic cell fraction substantiated that the most successful therapeutic effects have been observed for the mice treated with PTX-PU-FA (about 90% in PTX-PU-FA versus 75%, 60%, 15% in PTX-PU-TRAIL, PTX-PU, and Taxol® group respectively). CONCLUSIONS Using folate-targeted nanocarriers to treat cancers characterized by a high level of folate ligand expression is well substantiated by the findings of this study.
Collapse
|
14
|
Medvedeva NV, Prozorovskiy VN, Ignatov DV, Druzilovskaya OS, Kudinov VA, Kasatkina EO, Tikhonova EG, Ipatova OM. Pharmacological agents and transport nanosystems based on plant phospholipids. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s199075081503004x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Zhan M, Guo M, Jiang Y, Wang X. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy. Int J Mol Sci 2015; 16:14786-807. [PMID: 26140374 PMCID: PMC4519872 DOI: 10.3390/ijms160714786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/08/2015] [Accepted: 06/17/2015] [Indexed: 01/29/2023] Open
Abstract
The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.
Collapse
Affiliation(s)
- Minzhong Zhan
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Ming Guo
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Yanke Jiang
- Research Center of Medical Chemistry & Chemical Biology, Chongqing Technology and Business University, Chongqing 400067, China.
| | - Xiaomeng Wang
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| |
Collapse
|
16
|
Sanzhakov MA, Ignatov DV, Prozorovskiĭ VN, Druzhilovskaia OS, Medvedeva NV, Ipatova OM. [Development of targeted drug delivery system: synthesis of conjugates of address fragment (RA-COOH) with ligand (R-NH2)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 60:713-6. [PMID: 25552514 DOI: 10.18097/pbmc20146006713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
One of the main ways to increase the effectiveness of well-known medical formulations well-established in clinical medicine - development of delivery systems using new technological approaches and nanomaterials. Currently, much attention is given to targeted delivery systems. At the same time drug carrier has in addition to medication the so-called vector/address with a high affinity for binding to specific receptors on cells/tissue target. In this paper it is described the method for producing of address conjugates to over-expressed receptors on the tumor cells. As address fragment it was folic acid and as a linker was dodecylamine, causing inclusion the conjugate into lipid nanoparticles.
Collapse
|
17
|
Medvedeva N, Prosorovskiy V, Ignatov D, Druzilovskaya O, Kudinov V, Kasatkina E, Tikhonova E, Ipatova O. Pharmacological agents and transport nanosystems based on plant phospholipids. ACTA ACUST UNITED AC 2015; 61:219-30. [DOI: 10.18097/pbmc20156102219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A new generation of plant phosphatidylcholine (PC)-based pharmacological agents has been developed under academician A.I. Archakov leadership at the Institute of Biomedical Chemistry (IBMC). For their production a unique technology allowing to obtain dry lyophilized phospholipid nanoparticles of 30 nm was elaborated. The successful practical application of PC nanoparticles as a drug agent may be illustrated by Phosphogliv (oral and injection formulations). Being developed at IBMC for the treatment of liver diseases, including viral hepatitis, Phosphogliv (currently marketed by the “Pharmstandard” company) is approved for clinical application in 2000, and is widely used in medical practice. Based on the developed and scaled in IBMC technology of prerparation of ultra small size phospholipid nanoparticles without the use of detergents/surfactants and stabilizers another drug preparation, Phospholipovit, exhibiting pronounced hypolipidemic properties has been obtained. Recently completed preclinical studies have shown that PC nanoparticles of 20-30 nm activate reverse cholesterol transport (RCT) and in this context it is more active than well known foreign preparation Essentiale. Phospholipovit is now at the stage of clinical trials (phase 1 completed). PC was also used as a basis for the development of a transport nanosystem with a particles size of 20-25 nm in diameter and incorporation of various drug substances from various therapeutic groups. Using several drugs substances as an example, increased bioavailability and specific activity were demonstrated for the formulations equipped with such transport nanosystem. Formulations equipped with the transport nanosystems have been developed for such pharmacological agents as doxorubicin, rifampin, budesonide, chlorin E6, prednisone, and others.
Collapse
Affiliation(s)
| | | | - D.V. Ignatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - V.A. Kudinov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - O.M. Ipatova
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|