Initial Stages of Spontaneous Binding of Folate-Based Vectors to Folate Receptor-α Observed by Unbiased Molecular Dynamics

Molecular dynamics study of functionalized carbon nanotube loaded with multiple doxorubicin targeted to folate receptor α

Two novel targeted drug delivery systems (DDSs) were designed: folate (FOL) conjugated (9, 9) carbon nanotube (CNT) loaded with 20 doxorubicin (DOX) molecules (FOL-CNT/20DOX) and folate (FOL) conjugated carboxylated (9, 9) CNT (COOH-CNT) loaded with 24 doxorubicin (DOX) molecules (FOL-COOH-CNT/24DOX). The targeted property to folate receptor α (FRα) was calculated using molecular dynamics (MD) calculations. The structures of the FRα/FOL-CNT/20DOX and FRα/FOL-COOH-CNT/24DOX complexes were analyzed in detail. Radial distribution functions were calculated to analyze the distribution of DOX molecules around the CNTs in the complexes. The variation of representative distances and angles between novel DDSs and FRα, number of hydrogen bonds, and secondary structures of FRα during the MD simulations were studied to analyze the dynamic properties of the novel DDSs targeted to FRα. We further analyzed the root mean square displacement and root mean square fluctuation in detail. The results indicate that the two novel DDSs were very stable and well targeted with FRα, and FOL-COOH-CNT/24DOX had better targeting and stability than FOL-CNT/20DOX. This study is expected to provide insights for the design of efficient nano drug delivery systems with good FRα targeting and controllable drug loading dosage.

Characterization of the binding of the globular domains of the complement component C1q to phosphatidylserine

C1q, the key component of the classical pathway of the Complement system, is known for its vast functional activity including clearance of apoptotic cells. The binding of C1q to apoptotic blebs occurs via an interaction with the phosphatidylserine externalized on the cell surface. In this study, we characterized the interaction between C1q and phosphatidylserine, with emphasis on the structure of the phosphatidylserine-binding site within the globular domains of C1q and the nature of binding of C1q with phosphatidylserine, using both in vitro and in silico methods. We established that all three globular fragments, forming one C1q globular domain, bound phosphatidylserine with the leading role of the phosphatidylserine-binding site pertaining to the A chain of the globular fragment of C1q. We also determined the closest-contact amino acids of C1q participating in the interaction with phosphatidylserine. An important role is suggested for the glycosylated Asn124 residue in the A chain of the globular fragment.

Galectin-3 - A novel ligand of complement protein C1q

In the present study we report a novel interaction of human C1q, a primary activator of the Complement system, with human Galectin-3 (Gal-3). We investigated the potential recognition between C1q and Gal-3 on a solid hydrophobic surface by ELISA, by fluorescence spectroscopy, molecular docking and molecular dynamics (MD). The data showed that C1q and Gal-3 had a pronounced affinity for protein-protein interaction and supramolecular binding, locating the binding sites within the globular domains of C1q (gC1q) and on the backside of the carbohydrate recognition domain (CRD) of Gal-3. Fluorescence spectroscopy gave quantitative assessment of the recognition with KD value of 0.04 μM. MD analysis showed that when the active AAs of the two proteins interacted, electrostatic attraction, aided by a large number of hydrogen bonds, was dominant for the stabilization of the complex. When the contact of C1q and Gal-3 was not limited to active residues, the complex between them was stabilized mainly by Van der Waals interactions and smaller in number but stronger hydrogen bonds. This is the first report analyzing the interaction of Gal-3 with C1q, which could open the way to new applications of this protein-protein complex.

Molecular dynamics of JUNO-IZUMO1 complexation suggests biologically relevant mechanisms in fertilization

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.

Molecular Dynamics for the Optimal Design of Functionalized Nanodevices to Target Folate Receptors on Tumor Cells

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.

Study of folate-based carbon nanotube drug delivery systems targeted to folate receptor α by molecular dynamic simulations

We designed targeted drug delivery systems containing folate (FOL), the functionalized carbon nanotube (f-CNT) and doxorubicin (DOX), and studied the targeting properties of folate, f-CNT-FOL and DOX/f-CNT-FOL to folate receptor α (FRα). Folate was actively targeted to FRα in molecular dynamics simulations, and the dynamic process, effect of folate receptor evolution, and characteristics were analyzed. On this basis, the f-CNT-FOL and DOX/f-CNT-FOL nano-drug-carrier systems were designed, and the drug delivery process targeted to FRα was studied by 4 times MD simulations. The system evolution and detailed interactions of f-CNT-FOL and DOX/f-CNT-FOL with FRα residues were examined. We found that though the connection of CNT with the FOL could decrease the insertion depth of the pterin of FOL into the pocket of FRα, the loading of drug molecules could reduce this effect. Representative snapshots from the MD simulations were analyzed, showing that the location of DOX on the surface of CNT was constantly changed during the MD simulation, but the surface of the four rings of DOX were almost always parallel to the surface of CNT. The RMSD and RMSF were used to further analyze. The results may provide new insights for the design of novel targeted nano-drug-delivery systems.

Interaction mechanism of novel fluorescent antifolates targeted with folate receptors α and β via molecular docking and molecular dynamic simulations

Eight novel fluorescent antifolates were designed and docked with folate receptors FRα and FRβ. The structures of the complexes were further calculated by molecular dynamic (MD) simulations. The binding energies were calculated by molecular docking and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) studies. The binding energy differences between FRα and FRβ (|E_bα|-|E_bβ|) values for compounds 3 and 8 were 1.3 and 1.1 kcal/mol calculated by molecular docking, and 13.9 and 10.4 kcal/mol by MM-PBSA simulation, respectively. The results indicated that compounds 3 and 8 may be the best candidates for targeted drug delivery to FRα. The binding structures, interaction residues, negatively charged pocket volume, and surface area were analyzed for all the complexes. We further calculated the root mean square displacement and secondary structural elements of the bound complexes using molecular dynamics simulations. The purpose of this study is to design novel antifolates targeted to FRα and FRβ, and to further distinguish between cancer cells and inflammation.