Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview

Computational techniques have been applied in the drug discovery pipeline since the 1980s. Given the low computational resources of the time, the first molecular modeling strategies relied on a rigid view of the ligand-target binding process. During the years, the evolution of hardware technologies has gradually allowed simulating the dynamic nature of the binding event. In this work, we present an overview of the evolution of structure-based drug discovery techniques in the study of ligand-target recognition phenomenon, going from the static molecular docking toward enhanced molecular dynamics strategies

Pullulan Based Bioconjugates for Ocular Dexamethasone Delivery

Posterior segment eye diseases are mostly related to retinal pathologies that require pharmacological treatments by invasive intravitreal injections. Reduction of frequent intravitreal administrations may be accomplished with delivery systems that provide sustained drug release. Pullulan-dexamethasone conjugates were developed to achieve prolonged intravitreal drug release. Accordingly, dexamethasone was conjugated to similar to 67 kDa pullulan through hydrazone bond, which was previously found to be slowly cleavable in the vitreous. Dynamic light scattering and transmission electron microscopy showed that the pullulan-dexamethasone containing 1:20 drug/glucose unit molar ratio (10% w/w dexamethasone) self-assembled into nanoparticles of 461 +/- 30 nm and 402 +/- 66 nm, respectively. The particles were fairly stable over 6 weeks in physiological buffer at 4, 25 and 37 degrees C, while in homogenized vitreous at 37 degrees C, the colloidal assemblies underwent size increase over time. The drug was released slowly in the vitreous and rapidly at pH 5.0 mimicking lysosomal conditions: 50% of the drug was released in about 2 weeks in the vitreous, and in 2 days at pH 5.0. In vitro studies with retinal pigment epithelial cell line (ARPE-19) showed no toxicity of the conjugates in the cells. Flow cytometry and confocal microscopy showed cellular association of the nanoparticles and intracellular endosomal localization. Overall, pullulan conjugates showed interesting features that may enable their successful use in intravitreal drug delivery.Peer reviewe

A pH-sensitive stearoyl-PEG-poly(methacryloyl sulfadimethoxine)-decorated liposome system for protein delivery: an application for bladder cancer treatment

Stealth pH-responsive liposomes for the delivery of therapeutic proteins to the bladder epithelium were prepared using methoxy-poly(ethylene glycol)5kDa-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (mPEG5kDa-DSPE) and stearoyl-poly(ethylene glycol)-poly(methacryloyl sulfadimethoxine) copolymer (stearoyl-PEG-polySDM), which possesses an apparent pKa of 7.2. Liposomes of 0.2:0.6:100, 0.5:1.5:100 and 1:3:100 mPEG5kDa-DSPE/stearoyl-PEG-polySDM/(soybean phosphatidylcholine + cholesterol) molar ratios were loaded with bovine serum albumin (BSA) as a protein model. The loading capacity was 1.3% w/w BSA/lipid. At pH 7.4, all liposome formulations displayed a negative zeta-potential and were stable for several days. By pH decrease or addition to mouse urine, the zeta potential strongly decreased, and the liposomes underwent a rapid size increase and aggregation. Photon correlation spectroscopy (PCS) and transmission electron microscopy (TEM) analyses showed that the extent of the aggregation depended on the stearoyl-PEG-polySDM/lipid molar ratio. Cytofluorimetric analysis and confocal microscopy showed that at pH 6.5, the incubation of MB49 mouse bladder cancer cells and macrophages with fluorescein isothiocyanate-labelled-BSA (FITC-BSA) loaded and N-(Lissamine Rhodamine B sulfonyl)-1, 2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine triethylammonium salt (rhodamine-DHPE) labelled 1:3:100 mPEG5kDa-DSPE/stearoyl-PEG-polySDM/lipid molar ratio liposomes resulted in a time-dependent liposome association with the cells. At pH 7.4, the association of BSA-loaded liposomes with the MB49 cells and macrophages was remarkably lower than at pH 6.5. Confocal images of bladder sections revealed that 2 h after the instillation, liposomes at pH 7.4 and control non-responsive liposomes at pH 7.4 or 6.5 did not associate nor delivered FITC-BSA to the bladder epithelium. On the contrary, the pH-responsive liposome formulation set at pH 6.5 and soon administered to mice by bladder instillation showed that, 2 h after administration, the pH-responsive liposomes efficiently delivered the loaded FITC-BSA to the bladder epitheliu

Thin glass shells for active optics for future space telescopes

We present a method for the manufacturing of thin shells of glass, which appears promising for the development of active optics for future space telescopes. The method exploits the synergy of different mature technologies, while leveraging the commercial availability of large, high-quality sheets of glass, with thickness up to few millimeters. The first step of the method foresees the pre-shaping of flat substrates of glass by replicating the accurate shape of a mold via hot slumping technology. The replication concept is advantageous for making large optics composed of many identical or similar segments. After the hot slumping, the shape error residual on the optical surface is addressed by applying a deterministic sub-aperture technology as computer-controlled bonnet polishing and/or ion beam figuring. Here we focus on the bonnet polishing case, during which the thin, deformable substrate of glass is temporary stiffened by a removable holder. In this paper, we report on the results so far achieved on a 130 mm glass shell case study.Comment: This is a pre-print of an article published in CEAS Space Journal. The final authenticated version is available online at: http://link.springer.com/article/10.1007/s12567-019-00259-

Modeling and measurement of the scattering properties of the source pinhole in the BEaTriX facility

The purpose of this brief technical note is to provide an assessment of the performance of the tungsten pinhole placed in front of the microfocus Incoatec X-ray source with Titanium anode in the BEaTriX X-ray facility. The pinhole is a part of the collimator kit by Amptek purchased years ago to collimate a solid-state detector, and consists of a small (1/2 inch) tungsten disk with a 2.2 mm thickness and a 450 μm diameter. The pinhole is placed at a 20 mm distance from the source and limits the beam along the short arm of the facility, avoiding so the X-ray incidence on the tube walls which might cause unwanted X-ray reflection/scattering or diffuse background. At the same time, the pinhole located near the X-ray source provides visual reference for the parabolic mirror alignment. Pinholes are crucial optical components, as they have to diaphragm an X-ray beam without degrading it. Due to the closeness of the lateral walls of the pinhole to the X-rays, the surface has to be properly ruggedized in order to avoid unwanted reflections or diffuse scattering when X-rays impinge on it in grazing incidence conditions. Should this condition not be fulfilled, the pinhole would cause a broadening of the X- ray source and a consequent worsening of the finally collimated X-ray beam in BEaTriX. In this short note, we will show measurements of the X-ray beam in the BEaTriX facility aiming at ascertaining the scattering properties of the pinhole surface. The conclusion is that the amount of scattered/reflected radiation off the pinhole is hardly detectable and that the pinhole appears perfectly suitable for the collimation of the X-ray beam in the short arm of BEaTriX

Targeting Protein Kinase CK1\u3b4 with Riluzole: Could It Be One of the Possible Missing Bricks to Interpret Its Effect in the Treatment of ALS from a Molecular Point of View?

Riluzole, approved by the US Food and Drug Administration (FDA) in 1995, is the most widespread oral treatment for the fatal neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The drug, whose mechanism of action is still obscure, mitigates progression of the illness, but unfortunately with only limited improvements. Herein we report the first demonstration, using a combination of computational and in vitro studies, that riluzole is an ATP-competitive inhibitor of the protein kinase CK1 isoform\u2005\u3b4, with an IC50 value of 16.1\u2005\u3bcm. This allows us to rewrite its possible molecular mechanism of action in the treatment of ALS. The inhibition of CK1\u3b4 catalytic activity indeed links the two main pathological hallmarks of ALS: transactive response DNA-binding protein of 43\u2005kDa (TDP-43) proteinopathy and glutamate excitotoxicity, exacerbated by the loss of expression of glial excitatory amino acid transporter-2 (EAAT2)

Physical PEGylation to Prevent Insulin Fibrillation

Insulin is one of the most marketed therapeutic proteins worldwide. However, its formulation suffers from fibrillation, which affects the long-term storage limiting the development of novel devices for sustained delivery including portable infusion devices. We have investigated the effect of physical PEGylation on structural and colloidal stability of insulin by using 2 PEGylating agents terminating with polycyclic hydrophobic moieties, cholane and cholesterol: mPEG5kDa-cholane and mPEG5kDa-cholesterol, respectively. Microcalorimetric analyses showed that mPEG5kDa-cholane and mPEG5kDa-cholesterol efficiently bind insulin with binding constants (Ka) of 3.98 104 and 1.14 105 M-1, respectively. At room temperature, the 2 PEGylating agents yielded comparable structural stabilization of \u3b1-helix conformation and decreased dimerization of insulin. However, melting studies showed that mPEG5kDa-cholesterol has superior stabilizing effect of the protein conformation than mPEG5kDa-cholane. Furthermore, the fibrillation study showed that at a 1:1 and 1:5 insulin/polymer molar ratios, mPEG5kDa-cholesterol delays insulin fibrillation 40% and 26% more efficiently, respectively, as compared to mPEG5kDa-cholane which was confirmed by transmission electron microscopy imaging. Insulin was released from the mPEG5kDa-cholane and mPEG5kDa-cholesterol assemblies with comparable kinetic profiles. The physical PEGylation has a beneficial effect on the stabilization and shielding of the insulin structure into the monomeric form, which is not prone to fibrillation and aggregation

A Misdiagnosed Desmoplastic Neurotropic Melanoma of the Scalp: A Challenging Case for the Pathologist and Surgeon

Desmoplastic neurotropic melanoma (DNM) is a rare melanoma subtype that shows tropism for the nerves, perineural invasion correlates to higher rate of local recurrence, poorer prognosis and worse morbidity. Given the paucity of typical melanoma features, both clinical and pathological, this confusing skin cancer may act as a pretender, thus leading clinician to misdiagnosis and subsequent inappropriate conservative treatment. Sarcomatoid- like cells rearrangement and absence of pigmentation can lead towards sarcoma diagnosis, so specific skills are required to pathologist to properly recognize this melanoma subtype. In this case report, we present an example of how challenging can be the diagnosis, and how it can affect clinical outcom

A Misdiagnosed Desmoplastic Neurotropic Melanoma of the Scalp: A Challenging Case for the Pathologist and Surgeon

Desmoplastic neurotropic melanoma (DNM) is a rare melanoma subtype that shows tropism for the nerves, perineural invasion correlates to higher rate of local recurrence, poorer prognosis and worse morbidity. Given the paucity of typical melanoma features, both clinical and pathological, this confusing skin cancer may act as a pretender, thus leading clinician to misdiagnosis and subsequent inappropriate conservative treatment. Sarcomatoid- like cells rearrangement and absence of pigmentation can lead towards sarcoma diagnosis, so specific skills are required to pathologist to properly recognize this melanoma subtype. In this case report, we present an example of how challenging can be the diagnosis, and how it can affect clinical outcom