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Pralatrexate

Pralatrexate is a folate analogue antimetabolite used in the treatment of peripheral T-cell lymphoma.
It functions by inhibiting dihydrofolate reductase, thereby disrupting DNA synthesis and cellular proliferation.
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Most cited protocols related to «Pralatrexate»

A deep learning-based method, DFCNN (Dense fully Connected Neural Network), has been developed for predicting protein-drug binding probability [15 (link)] and used in this paper for the initial drug screening (Fig 1A). DFCNN utilizes the concatenated molecular vector of protein pocket and ligand as input representation, and the molecular vector are generated by Mol2vec [29 (link)] which is inspired by the word2vec model in natural language processing. DFCNN model was trained on a dataset extracted from PDBbind database [30 (link)]. Negative data samples in the dataset were generated by cross-combination of proteins and ligands from PDBbind database and positive data samples were taken from protein-ligand pairs in experimental structure. The details of the method were described in our previous paper [15 (link)], and DFCNN achieved an AUC value around 0.9 for the independent testing set [15 (link)]. The model is about ~100,000 times faster than Autodock Vina in predicting protein-ligand binding probability (range 0~1), because it does not rely on the protein-drug complex conformation.
We screen a large scale chemical compound dataset (about 10 million compounds) targeting 8 representative protein targets taken from the DUD.E diverse data set in order to examine the efficiency and effectiveness of the DFCNN method. For each target, the corresponding dataset contains some active compounds (between 40 and 536) in the DUD.E dataset and 10,402, 895 drug-like compounds from ZINC database. The effectiveness is measured by the prediction-random ratio (Ratio0.9), defined as TPR0.9/Random0.9, where TPR0.9 indicates the ratio (N0.9/Active_num) between the number of active compounds with a DFCNN score larger than 0.9 (N0.9) and the active number of compounds (Active_num). The total number of the compounds (Total_num) with score above 0.9 is defined as NN. The random selection rate (Random0.9) is defined as NN/Total_num. Using cutoff score of 0.9, the prediction-random ratio measures the ratio of predicted TPR and random selection TPR.
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Publication 2020
Binding Proteins Cloning Vectors Compounds, Zinc Ligands Pharmaceutical Preparations Proteins Protein Targeting, Cellular
Further drug screening was carried out by force field based molecular dynamic (MD) simulations. The initial protein-drug complexes was from top score conformation Autodock Vina docking, the ligand was edited by pymol software [32 ] to make it in correct protonation state at pH 7. In this study, we selected 14 drug binding complexes for MD simulation, including Adenosine, Amenamevir, Amoxicillin, Azithromycin, Clofarabine, Fipronil, Gemcitabine, Nitisinone, Pralatrexate, Raltegravir, Romidepsin, Sofosbuvir, Teriflunomide and Vidarabine, respectively.
We also refined a pocket molecular dynamics simulation (pocket MD, S11B Fig) to facilitate the simulation process by only keeping the binding pocket region for simulation. Binding free energy calculation can be estimated by metadynamics simulations to explore whether protein-ligand will bind in solution. Metadynamics relies on addition of a bias potential to sample the free energy landscape along a specific collective variable of interest [33 (link),34 (link)]. Note that the binding free energy calculations from Metadynamics may only be suitable for detect the general trend of binding in virtual screening.
The pocket MD is same as the classical MD simulation, except that we only using the pocket region to reduce system size for simulation (S11B Fig), which is inspired by a previous dynamic undocking (DUck) method [35 (link)]. An in-house script was used to extract the pocket region of the protein (1nm within the binding ligand), the N terminal and C terminal ends were capped with the ACE and NHE terminals, respectively. We applied a position restrain to the ACE and NHE terminals to maintain the relative conformation of the pocket. MD simulation was carried out by Gromacs with AMBER-99SB force field [36 ,37 (link)]. The topology of ligand and the partial charges of ligand was generated by ACPYPE [38 (link)], which relies on Antechamber [39 (link)]. Firstly, we created a dodecahedron box and put the target-ligand complex at the center. A minimum distance from the protein to box edge was set to 1 nm. We filled the dodecahedron box with TIP3P water molecules [40 (link)], the counter ions were added to neutralize the total charge using the Gromacs program tool [41 (link)]. The long-range electrostatic interactions under the periodic boundary conditions was calculated with Particle Mesh Ewald approach [42 (link)]. A cutoff of 14 Å was used for van der Waals non-bonded interactions. Covalent bonds involving hydrogen atoms were constrained by applying the LINCS algorithm [43 (link)].
We performed the energy minimization steps with a step-size of 0.001ns, 100 ps simulation with isothermal-isovolumetric ensemble (NVT), and 10ns simulation with isothermal-isobaric ensemble (NPT) for water equilibrium. After that, a 100ns NPT production run (step size 2 fs) was carried out. The Parrinello-Rahman barostat and the modified Berendsen thermostat were used for simulation with a fixed temperature of 308 K and a pressure of 1 atm. RMSD and hydrogen bond number of the trajectory were calculated using Gromacs tools.
The simulation was continued using the metadynamics approach for exploring the free energy landscape. The interface coordination number of atoms of protein ligand complex was used as collective variable (CV). The protein-ligand interface coordination numbers correlate with the numbers of atom contact, and larger coordination number usually indicates that protein-ligand is in binding state.
The coordination number C is defined as follows by Plumed:
C=iAjBSij
and
Sij=1(rijd0r0)n1(rijd0r0)m
In the simulation, n was 6, m was 12, d0 was 0 nm and r0 was 0.5 nm. d0 is a parameter of the switching function. rij is the distance between atom i and atom j. The degrees of contacts between two groups of atoms can be estimated by above function(1) [44 (link)]. Metadynamics simulation for each protein-ligand system was performed for 100 ns (except protein-Azithromycin, which was extended to 300ns in order to reach the 0 Coordination Number and achieve convergences). During the metadynamics simulation, Gaussian values were deposited every 1 ps with a height of 0.3 kJ/mol. The widths of the Gaussians were 5 for the coordination number. The free energy landscapes of the metadynamics simulations along the CV were generated by the Plumed program and plotted using Gnuplot [45 ].
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Publication 2020
Tritiated pralatrexate, pemetrexed (both generally labeled), and [3′,5′,7-3H]MTX were obtained from Moravek Biochemicals (Brea, CA). Pemetrexed and MTX purity was established and monitored by high-performance liquid chromatography (HPLC) as described previously [24 (link)]. Pralatrexate purity was monitored using a 5 mm OSD2 4.6 × 250 mm reversed phase high-performance liquid chromatography column (Waters Spherisorb), by isocratic elution with 100 mM sodium acetate pH 5.5 (solvent A) and 15% acetonitrile (solvent B). The mobile phase was delivered at 1 ml/min, reaching 100% solvent B in 30 min. Nonlabeled MTX was obtained from Sigma-Aldrich (St. Louis, MO), nonlabeled (6S)5-formyltetrahydrofolate (5-formylTHF) from Schircks Laboratories (Jona, Switzerland) and nonlabeled pemetrexed from LC Laboratories (Woburn, MA). Pralatrexate was obtained from Spectrum Pharmaceuticals (Irvine, CA).
Publication 2013
acetonitrile Chromatography, Reversed-Phase Liquid High-Performance Liquid Chromatographies N(5)-Formyltetrahydrofolate Pharmaceutical Preparations pralatrexate Sodium Acetate Solvents
Survival outcome (overall survival [OS]) data from four centers with prospectively collecting data on patients with PTCL in the United States, Europe, and Korea were acquired. Data were collected from 1) Memorial Sloan Kettering Cancer Center (MSKCC) for 171 patients who were treated at their institution between June 1997 to July 2011, 2) University of Nebraska Medical Center (UNMC) provided data for 67 patients diagnosed between July 1, 1984 and May 17, 2010 who were part of the Nebraska Lymphoma Study Group, 3) Groupe d’Etude des Lymphomes de l’Adulte (GELA) provided information on 117 patients whose first-line treatment was administered under the four clinical trials conducted between December 1997 and April 2008, and 4) The Samsung Medical Center (SMC) in South Korea provided data on 504 patients based on a retrospectively characterized databased collected between 1995 and 2007 and a prospectively maintained database initiated in 2008. In total, data from 859 patients were collected from the four sites.
A total of 386 patients (including 69, 44, 110, and 163 patients collected from MSKCC, UNMC, GELA, and SMC databases, respectively) were identified from these four databases based on the following specific selection criteria: 1) histologies consistent with the inclusion criteria of PROPEL; 2) patients who received at least two lines of prior therapy (ie, the second line of therapy would match with patients receiving pralatrexate on PROPEL, which required one line of prior therapy); and 3) patients who had not received pralatrexate. The efficacy data were not part of the criteria to select patients for inclusion in the historical database.
Publication 2018
Lymphoma Malignant Neoplasms Patients pralatrexate Therapeutics
Among the patients evaluable for efficacy in PROPEL, three analysis sets were identified to investigate the overall response rate (ORR), complete remission (CR), PFS, and duration of response (DOR) based on the number of prior line of treatment, including 1) patients (n = 23) who had received one prior systemic therapy, 2) patients (n = 29) who had received two prior systemic therapies, and 3) patients (n = 57) who had received at least three prior systemic therapies.
The von Hoff analysis (10 (link),15 (link),16 (link)), compares the PFS on the study treatment to the PFS on the line of therapy before. The analysis is predicated on the idea that successive lines of therapy almost never produce a benefit greater than the lines of treatment before. Thus, the statistics of the analysis are defined as PFS on the experimental drug / PFS for the line of therapy just before, with a ratio greater than 1.3 being considered statistically significant, where the hypothesis would miss up to 15% for PFS ratio more than 1.3. The Von Hoff analysis was performed on the subset of patients with refractory disease (n = 68) that responded to pralatrexate treatment (n = 16).
Publication 2018
Patients Pharmacotherapy pralatrexate

Most recents protocols related to «Pralatrexate»

Example 1

Production of Alpha Hexaglutamated Pemetrexed (αHgPMX) Liposomes

Briefly L alpha hexaglutamated pemetrexed (aGR6) and D alpha hexaglutamated pemetrexed (aDGR6) were encapsulated in liposomes by the following procedure. First, the lipid components of the liposome membrane were weighed out and combined as a concentrated solution in ethanol at a temperature of around 65° C. In this example, the lipids used were hydrogenated soy phosphatidylcholine, cholesterol, and DSPE-PEG-2000 (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (polyethylene glycol)-2000]). The molar ratio of HSPC:Cholesterol:PEG-DSPE was approximately 3:2:0.15. Next, the aGR6 or aDGR6 was dissolved in 5% dextrose at a concentration of 150 mg/ml with a pH of 6.5-6.9. The drug solution was heated up to 65° C. The ethanolic lipid solution was injected into the aGR6 or aDGR6 solution using a small-bore needle. During this step the drug solution was well stirred using a magnetic stirrer. The mixing was performed at an elevated temperature (63° C.-72° C.) to ensure that the lipids were in the liquid crystalline state (as opposed to the gel state that they attain at temperatures below the lipid transition temperature Tm=51° C.−54° C.). As a result, the lipids were hydrated and form multiple bilayer (multilamellar) vesicles (MLV) containing aGR6 or aDGR6 in the aqueous core.

Downsizing of MLV's Using Filter Extrusion

The MLVs were fragmented into unilamellar (single bilayer) vesicles of the desired size by high-pressure extrusion using three passes through stacked (track-etched polycarbonate) membranes. The first pass was performed through stacked membranes consisting of two layers with a pore size of 200 nm. The remaining two passes were through the stacked membranes consisting of three layers with a pore size of 100 nm. During extrusion, the temperature was maintained above the Tm to ensure plasticity of the lipid membranes. As a result of the extrusion, large and heterogeneous in size and lamellarity MLVs turned into small, homogenous (90-125 nm) unilamellar vesicles (ULV) that sequestered the drug in their interior. A Malvern Zetasizer Nano ZS instrument (Southborough, Mass.) with back scattering detector(90°) was used for measuring the hydrodynamic size (diameter) at 25° C. in a quartz micro cuvette. The samples were diluted 50-fold in formulation matrix before analysis.

Purification of Liposomes

After the ULV's containing aGR6 or aDGR6 had been produced, the extra-liposomal free drug was removed using columns for small volume or tangential flow diafiltration against a suitable buffer for large volume. Although any buffer solution can be used, in this example the buffer used was 5 mM HEPES, 145 mM Sodium Chloride, pH 6.7. Upon completion of purification, filter sterilization was performed using a 0.22 micron filter.

Production of Alpha Hexaglutamated Pemetrexed (αHgPTX) Liposomes

Briefly L alpha hexaglutamated pemetrexed (aG6) and D alpha hexaglutamated pemetrexed (aDG6) were encapsulated in liposomes by the following procedure. First, the lipid components of the liposome membrane were weighed out and combined as a concentrated solution in ethanol at a temperature of around 65° C. In this example, the lipids used were hydrogenated soy phosphatidylcholine, cholesterol, and DSPE-PEG-2000 (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (poly-ethylene glycol)-2000]). The molar ratio of HSPC:Cholesterol:PEG-DSPE was approximately 3:2:0.15. Next, the aG6 or aDG6 was dissolved in 5% dextrose at a concentration of 150 mg/ml with a pH of 6.5-6.9. The drug solution was heated up to 65° C. The ethanolic lipid solution was injected into the aG6 or aDG6 solution using a small-bore needle. During this step the drug solution was well stirred using a magnetic stirrer. The mixing was performed at an elevated temperature (63° C.-72° C.) to ensure that the lipids were in the liquid crystalline state (as opposed to the gel state that they attain at temperatures below the lipid transition temperature Tm=51° C.-54° C.). As a result, the lipids were hydrated and form multiple bilayer (multilamellar) vesicles (MLV) containing aG6 or aDG6 in the aqueous core.

Downsizing of MLV's Using Filter Extrusion

The MLVs were fragmented into unilamellar (single bilayer) vesicles of the desired size by high-pressure extrusion using three passes through stacked (track-etched polycarbonate) membranes. The first pass was performed through stacked membranes consisting of two layers with a pore size of 200 nm. The remaining two passes were through the stacked membranes consisting of three layers with a pore size of 100 nm. During extrusion, the temperature was maintained above the Tm to ensure plasticity of the lipid membranes. As a result of the extrusion, large and heterogeneous in size and lamellarity MLVs turned into small, homogenous (90-125 nm) unilamellar vesicles (ULV) that sequestered the drug in their interior. A Malvern Zetasizer Nano ZS instrument (Southborough, Mass.) with back scattering detector(90°) was used for measuring the hydrodynamic size (diameter) at 25° C. in a quartz micro cuvette. The samples were diluted 50-fold in formulation matrix before analysis.

Purification of Liposomes

After the ULV's containing aG6 or aDG6 had been produced, the extra-liposomal gG6 was removed using columns for small volume or tangential flow diafiltration against a suitable buffer for large volume. Although any buffer solution can be used, in this example the buffer used was 5 mM HEPES, 145 mM Sodium Chloride, pH 6.7. Upon completion of purification, filter sterilization was performed using a 0.22 micron filter. The typical characteristics of liposomal derivatives are shown in the table below.

StartingEncapsulationFinalDrug/LipidZeta
con.efficiencycon.RatioDiameterPDIpotential
Lps aDG61mg/ml4.75%0.031mg/ml25-30g/mM lipids122.8nm0.021−1.14 mV
Lps aG61mg/ml5.90%0.039mg/ml25-30g/mM lipids100.2nm0.018−1.90 mV
LpS aG6150mg/ml36%8.0mg/ml230-260g/mM Lipids104nm0.04−2.73 mV
Dose Response Study of Alpha HGP (Hexaglutamated Pemetrexed) and Liposomes

A dose response study was performed using liposomes containing hexaglutamated pemetrexed that were prepared essential as described above.

Cell viability was determined by CellTiter-Glo® (CTG) luminescent cell viability assay on Day 3 (48 hour) and Day 4 (72 hour). This assay determines the number of viable cells in culture based on quantifying ATP that is present within, which in turn signals the presence of metabolically active cells. The CTG assay uses luciferase as a readout. To assess cell viability Dose response inhibition of pemetrexed, HGP and liposomes on different cancer cell growth were investigated using CellTiter-Glo® luminescent cell viability assay. Human cancer cells were harvested, counted and plated at a same cell density on Day 0. A series of 8 dilutions of each test article were added to the cells on Day 1. Dose response curve were generated and fit using GraphPad Prism and IC50 of each test article were calculated. A lower the IC50 is, the more potent the test article is in term of cancer cell growth inhibition.

Cells were seeded into 96-well plate at a cell density of 5×104 cells per well in 100 μl of fresh media on Day 0. Eight serial 2-fold dilutions of each test article in culture medium were generated and added to cells in triplicate on Day 1. In addition, three wells of cells were treated with vehicle (HBS for free drug or empty liposome for liposomal HGP) alone as a control.

On Days 3 and 4, 100 μl of CellTiterGlo® Reagent were added to each well and incubated at room temperature for 15 minutes. Luciferase luminescence were recorded for each well. In addition, 8 serial 2-fold dilutions of the vehicle (HBS or empty liposome) in culture medium were added into empty wells and included in the assay to generate the background luminescence signals. Luciferase signals were normalized by subtracting the background luminescence signal out of the read-outs respectively.

Human Normal Primary Bone Marrow CD34+ Cells were obtained from ATCC. (ATCC Catalog Number PCS-800-012). Cells were thawed at 37° C. for 1 minute and then placed on ice. The cells were then resuspended in StemSpan SFEM (Stem Cell Tech Catalog Number 9650) plus 10% heat inactivated fetal bovine serum (Corning 35-015-CV). The cells were plated into 96 well culture plates at a density of 2.5×104 cells/well. The following day, live cells were collected via centrifugation and resuspended in neutrophil growth media (StemSpan SFEM plus 10% Heat Inactivated fetal bovine serum plus 100 ng/ml human stem cell factor (Sigma Catalog Number H8416), 20 ng/ml human granulocyte colony-stimulation factor (Sigma Catalog Number H5541), and 10 ng/ml human recombinant IL3 (Sigma SRP3090) at a density of 2.5×104 cells/well. Cells were incubated at 37° C. for 10 days. Fresh media was added every two days. Mature neutrophils were then collected and plated in 96 well plates at a density of 1×104 cells/well and incubated at 37° C. overnight. The next day, test article or vehicle was resuspended in neutrophil growth media and added to the plates. The cells were then incubated for either 48 hours or 72 hours at 37° C. and then assayed at each time point using the Cell Titer Glo Assay (Promega Catalog #G7572).

Methodologies used for cell line AML12 (non-cancerous liver cells) and CCD841 (non-cancerous colon epithelial cells) are similar to the methods used for cancer cells.

Results

In a set of dose response experiments, 6 cell lines representing different types of cancers, namely HT-29 (colon cancer), H2342 (NSCLC, adenocarcinoma subtype), H292 (NSCLC, adenocarcinoma subtype), SW620 (CRC), H1806 (triple negative breast cancer) and OAW28 (ovarian cancer), were studied (FIG. 2). Treatment consisted of exposure for 48 hours using 2 different encapsulated derivatives of liposomal alpha pemetrexed hexaglutamate, namely liposomal alpha L hexaglutamate (liposomal aG6) and its mirror image, liposomal alpha D hexaglutamate (liposomal aDG6) also referred to as its corresponding enantiomer.

The relative potency of the above mentioned derivatives as compared to pemetrexed, following exposure over 48 hours, is represented in FIG. 2. The relative potency of treatment using the various derivatives, as shown in this figure was calculated by dividing the IC50 of pemetrexed by the IC50 of the liposomal alpha pemetrexed hexaglutamate for each cell line. As shown in this figure, in all cell lines, the potency of liposomal alpha pemetrexed hexaglutamate well exceeded that of pemetrexed. By way of example, consider the NSCLC cell line H292. As shown in the figure, the potency of liposomal alpha pemetrexed hexaglutamate was ≥50-fold that of pemetrexed. This suggests that a 2% or lower dose of the liposomal alpha pemetrexed hexaglutamate could have the same treatment effect as a 100% dose of pemetrexed.

As stated in some instances increased uptake of payload can be achieved by targeting the liposomal delivery vehicle using antibody such as Folate Receptor Alpha. By way of example in the next two experiments Liposomal L Gamma G6/Lps Hexa gG6 was encapsulated using the methods previously described above. Subsequently, pemetrexed, liposomal gamma pemetrexed hexaglutamate derivatives (Liposomal L gamma G6/Lps Hexa gG6) and Folate Receptor Alpha Targeted Liposomal L Gamma G6 (Liposomal gG6-FR1Ab), Free (unencapsulated) L gamma G6 were tested for cytotoxic activity on representative cell lines in non small cell lung cancer cells (NCI-H2342) and colorectal cancer cells (HT-29) as shown in FIG. 3 and FIG. 4 respectively. These data show that both liposomal L gamma pemetrexed hexaglutamate and Folate Receptor Alpha Targeting liposomal L gamma pemetrexed hexaglutamate are more potent than pemetrexed in both cell lines. In general Folate Receptor Alpha Antibody targeting liposomes show the highest potency. By contrast free L gamma G6 has the lowest potency due to its inability to traffic across cell membranes effectively.

Cancer cell viability studies comparing the liposomal alpha pemetrexed hexaglutamate derivatives (liposomal L alphaG6/Lps Hexa aG6 and liposomal D alphaG6/Lps Hexa aDG6) and pemetrexed for cytotoxic activity on representative cell lines in breast, lung and ovarian cancer are shown in FIGS. 5-7. These data show that both liposomal alpha L pemetrexed hexaglutamate and liposomal alpha D pemetrexed hexaglutamate are more potent than pemetrexed. Further, as an indicator of efficacy, the results of the experiments on the same cell lines depicted at various dose levels ranging from 16 to 128 nM in FIGS. 8-10. As shown in these figures, at each of these dose ranges, liposomal alpha L pemetrexed hexaglutamate and liposomal alpha D pemetrexed hexaglutamate are superior to pemetrexed in terms of inhibiting cancer cells for the lung and breast cancer cell lines. In the ovarian cancer cell line, pemetrexed at the dose of 128 nM, appears to be equally effective as liposomal alpha pemetrexed hexaglutamate, whereas the liposomal alpha pemetrexed hexaglutamate at the dose of 32 nM and 64 nM has a better treatment effect than pemetrexed; at 16 nM the treatment effect is lower and similar in magnitude for liposomal alpha pemetrexed hexaglutamate and pemetrexed.

The major toxicities seen in patients treated with pemetrexed is bone marrow suppression which manifests as a decrease in blood counts including neutrophil counts (a type of white blood cells). There is also some adverse effect on the lining of the mouth and gut that manifests as diarrhea and mucositis, as well as an adverse effect on the liver in some instances. To assess the above-mentioned toxicities, treatment of the liposomal alpha pemetrexed hexaglutamate derivatives (L and D) and pemetrexed was measured at 48 hours on CD34+ cells that were differentiated into neutrophils, CCD841 colon epithelium cells and AML12 liver cells. As shown in FIG. 11, liposomal alpha pemetrexed hexaglutamate is significantly less toxic to differentiating human neutrophils in contrast to pemetrexed. This is also supported by neutrophil counts that are better preserved following treatment with the liposomal alpha L pemetrexed hexaglutamate or liposomal alpha D pemetrexed hexaglutamate compared to pemetrexed, at dose ranges from 16 nM to 128 nM (FIG. 12). Strikingly, there does not appear to be any toxicity to the liver cells following treatment with liposomal L alpha pemetrexed hexaglutamate or liposomal alpha D pemetrexed hexaglutamate at the dose levels studied (FIG. 13). In contrast, pemetrexed at all doses studied is leading to a reduction in the liver cell counts of approximately 40%. And finally, the same trend is seen following treatment of epithelial colon cells (FIG. 14). As shown in this figure, pemetrexed at all doses studied is leading to approximately a ≥50% decrease in the number of cells compared to approximately a 20% or less decrease after treatment with liposomal alpha L pemetrexed hexaglutamate and liposomal alpha D pemetrexed hexaglutamate.

Example 3

Methods

Production of Targeted Gamma Hexaglutamated Pemetrexed (HGP) Liposomes

Gamma HGP (gG6) was encapsulated in liposomes and the liposomes were downsized and purified according to procedures essentially as set forth above in Example 1.

Antibody Conjugation

Activated liposomes were prepared by adding DSPE-PEG-maleimide to the lipid composition. The liposomes contain four different lipids: hydrogenated soy phosphatidylcholine (HSPC), cholesterol, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (DSPE-PEG-2000), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[maleimide (polyethylene glycol)-2000] (DSPE-PEG-maleimide), in ratios of 3:2:0.1125:0.0375.

Antibody thiolation was accomplished through use of Traut's reagent (2-iminothiolane) to attach a sulfhydryl group onto primary amines Antibody was suspended in PBS at a concentration of 0.9-1.6 mg/ml. Traut's reagent (14 mM) was added to antibody solution at a final concentration of 1-5 mM and then removed through dialysis after one-hour incubation at room temperature. Thiolated antibody was added to activated liposomes at a ratio of 60 g/mol phosphate lipids, and the reaction mixture was incubated for one hour at room temperature and over-night at 4 uL-cysteine was used to terminate the reaction and unconjugated antibody was removed through dialysis.

Exemplary direct and post insertion antibody-liposome conjuation methods are provided below.

Exemplary Antibody Conjugation Method 1: Direct Conjugation

Antibody or its fragments, such as Fab or scFv, can be conjugated directly onto thiol-reactive liposome. Thiol-reactive liposomes are prepared by adding DSPE-PEG-maleimide to the lipid composition. The liposomes contain four different lipids: hydrogenated soy phosphatidylcholine (HSPC), cholesterol, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (DSPE-PEG-2000), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[maleimide (polyethylene glycol)-2000] (DSPE-PEG-maleimide), in ratios of 3:2:0.1125:0.0375.

Antibody (or its fragments, such as Fab or scFv) thiolation is accomplished through use of Traut's reagent (2-iminothiolane) to attach a sulfhydryl group onto primary amines Antibody (or its fragment) is suspended in PBS at a concentration of 0.9-1.6 mg/ml. Traut's reagent (14 mM) is added to antibody (or its fragment) solution at a final concentration of 1-5 mM and then removed through dialysis after one-hour incubation at room temperature. Thiolated antibody (or its fragment) is added to thiol-reactive liposome at a ratio of 60 g/mol phosphate lipids, and the reaction mixture is incubated for one hour at room temperature and over-night at 4° C. L-cysteine is used to terminate the reaction and unconjugated antibody (or its fragment) is removed through dialysis.

Antibody or its fragments, such as Fab or scFv, which contains a cysteine residue at the C-terminal can be conjugated directly onto the liposome by incubating a reduced antibody (or its fragment) with thiol-reactive liposome. Antibody (or its fragment) with a cysteine tail is dissolved and reduced by a 10-20 mM reducing reagent (such as 2-mercaptoethylamine, cysteine, or dithioerythritol) at pH<7. The excess reducing reagent is removed thoroughly by size exclusion chromatography or dialysis. The purified and reduced antibody (or its fragment) can be directly conjugated to the thiol-reactive liposome.

Exemplary Antibody Conjugation Method 2: Post Insertion

Antibody or its fragments, such as Fab or scFv, which contains a cysteine residue at the C-terminal can be conjugated and incorporated into the liposome through a “post insertion” method. Micelles of thiol-reactive lipopolymer (such as DSPE-PEG-maleimide) is prepared by dissolving in an aqueous solution at 10 mg/ml. Antibody (or its fragment) with a cysteine tail is dissolved and reduced by a 10-20 mM reducing reagent (such as 2-mercaptoethylamine, cysteine, or dithioerythritol) at pH<7. The excess reducing reagent is removed thoroughly by size exclusion chromatography or dialysis. The purified and reduced antibody (or its fragment) is then incubated with the micelles of thiol-reactive lipopolymers at a molar ratio of 1:4. At the end of the reaction, the excess maleimide groups are quenched by a small amount of cysteine (1 mM) or mercaptoethanol. Unconjugated antibody (or its fragment) is removed by size exclusion chromatography. Purified conjugated micelles is then incubated with liposome at 37° C. or elevated temperature.

Physical Characteristics of the Nanoparticles

StartingEncapsulationFinalDrug/LipidZeta
con.efficiencycon.RatioDiameterPDIpotential
Lps gG620 mg/ml10.60%1.39 mg/ml35-50 g/mM lipids114.9 nm0.035−1.76 mV
Dose response study of HGP (pentaglutamated pemetrexed) and liposomes.

Cell viability was determined by CellTiter-Glo® (CTG) luminescent cell viability assay on Day 3 (48 hour) and Day 4 (72 hour). This assay determines the number of viable cells in culture based on quantifying ATP that was present within, which in turn signals the presence of metabolically active cells. The CTG assay uses luciferase as a readout. To assess cell viability Dose response inhibition of pemetrexed, HGP and liposomes on different cancer cell growth were investigated using CellTiter-Glo® luminescent cell viability assay. Human cancer cells were harvested, counted and plated at a same cell density on Day 0. A series of 8 dilutions of each test article were added to the cells on Day 1. Dose response curve were generated and fit using GraphPad Prism and IC50 of each test article were calculated. A lower the IC50 is, the more potent the test article was in term of cancer cell growth inhibition.

Cells were seeded into 96-well plate at a cell density of 5×104 cells per well in 100 μl of fresh media on Day 0. Eight serial 2-fold dilutions of each test article in culture medium were generated and added to cells in triplicate on Day 1. In addition, three wells of cells were treated with vehicle (HBS for free drug or empty liposome for liposomal HGP) alone as a control.

On Days 3 and 4, 100 μl of CellTiterGlo® Reagent were added to each well and incubated at room temperature for 15 minutes. Luciferase luminescence were recorded for each well. In addition, 8 serial 2-fold dilutions of the vehicle (HBS or empty liposome) in culture medium were added into empty wells and included in the assay to generate the background luminescence signals. Luciferase signals were normalized by subtracting the background luminescence signal out of the read-outs respectively.

Human Normal Primary Bone Marrow CD34+ Cells were obtained from ATCC. (ATCC Catalog Number PCS-800-012). Cells were thawed at 37° C. for 1 minute and then placed on ice. The cells were then resuspended in StemSpan SFEM (Stem Cell Tech Catalog Number 9650) plus 10% heat inactivated fetal bovine serum (Corning 35-015-CV). The cells were plated into 96 well culture plates at a density of 2.5×104 cells/well. The following day, live cells were collected via centrifugation and resuspended in neutrophil growth media (StemSpan SFEM plus 10% Heat Inactivated fetal bovine serum plus 100 ng/ml human stem cell factor (Sigma Catalog Number H8416), 20 ng/ml human granulocyte colony-stimulation factor (Sigma Catalog Number H5541), and 10 ng/ml human recombinant IL3 (Sigma SRP3090) at a density of 2.5×104 cells/well. Cells were incubated at 37° C. for 10 days. Fresh media was added every two days. Mature neutrophils were then collected and plated in 96 well plates at a density of 1×104 cells/well and incubated at 37° C. overnight. The next day, test article or vehicle was resuspended in neutrophil growth media and added to the plates. The cells were then incubated for either 48 hours or 72 hours at 37° C. and then assayed at each time point using the Cell Titer Glo Assay (Promega Catalog #G7572).

Methodologies used for cell line AML12 (non-cancerous liver cells) and CCD841 (non-cancerous colon epithelial cells) are similar to the methods used for cancer cells.

Results:

The dose response relationship of free pemetrexed gamma hexaglutamate (gG6), (non-targeted) liposomal gamma hexaglutamate (liposomal gG6), pemetrexed and folate receptor alpha targeting antibody (FR1Ab) liposomal pemetrexed gamma hexaglutamate (liposomal gG6-FR1Ab), in the NCI H2342 non-small cell lung cancer (NSCLC), adenocarcinoma subtype is shown in FIG. 3. The output is percentage of viable cells after 48 hours of treatment as measured by luciferase luminescence. As shown in this FIG. 3, the free pemetrexed gG6 appears to be the least potent as measured by IC50. Both the liposomal pemetrexed gG6 and the liposomal pemetrexed gG6-FR1Ab are 7-fold and 40-fold more potent, respectively, than free pemetrexed.

Similar data is shown for the HT-29 colon cancer cell line in FIG. 4 that depict cell viability expressed as a percentage. As shown in this figure, free pemetrexed gG6 appears to be the least potent. In this instance, the liposomal pemetrexed gG6 is twice as potent as pemetrexed and the liposomal pemetrexed gG6-FR1Ab is 5-fold more potent than free pemetrexed.

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Patent 2023
Pharmacokinetic (PK) studies were performed during the part 2 of the study and included collection of blood samples for PK analysis of pralatrexate for the first 12 patients at before injection, end of injection, and 0.5, 1, 3, 6, 10, 16, and 24 hours after the end of pralatrexate injection during cycle 1, dose 1.
Pralatrexate comprised a mixture of R- and S-diastereomeric folate derivatives and, as folate, has an important role in cell growth and proliferation.21 (link) The characterization of the plasma concentrations of pralatrexate (S-Diastereomer [PDX-10a] and R-Diastereomer [PDX-10b]) was a key secondary objective, determined using a validated LC-MS/MS bioanalytical method. PK parameters of pralatrexate (PDX-10a and PDX-10b) were calculated based on respective drug concentration–time data by a noncompartmental method using Phoenix WinNonlin (Certara, Princeton, NJ) version 8.3.1 or higher. The following PK parameters of pralatrexate (PDX-10a and PDX-10b) were estimated: area under the curve, rate of absorption, Tmax, total clearance, T1/2, and volume of distribution.
Publication 2023
In part 1 of this study, patients were enrolled in a traditional 3 + 3 dose-escalation scheme, starting with dose level 1, with dose escalation as shown in supplemental Table 1. Pralatrexate was administered at 10, 15, 20, 25, or 30 mg/m2 as an IV on days 1 and 8 of a standard 21-day CHOP regimen (cyclophosphamide 750 mg/m2, doxorubicin 50 mg/m2, and vincristine 1.4 mg/m2 [maximum, 2 mg] on day 1 and oral prednisone 100 mg on days 1-5).
A DLT was defined as an adverse event (AE) that, because of its type, severity, or relationship to study drug, must be counted toward determining the MTD. For purposes of determining the MTD of pralatrexate (Folotyn; Acrotech Biopharma, East Windsor, NJ) plus CHOP (Fol-CHOP) treatment, AEs that were considered DLTs when they occurred during the first treatment cycle included severe infections (grade 4); grade 4 neutropenia lasting for ≥7 days despite granulocyte colony-stimulating factor administration; any grade 4 thrombocytopenia or any grade thrombocytopenia with clinically significant bleeding (excluding epistaxis); or grade ≥3 study treatment-related nonhematologic toxicity, excluding nausea/vomiting in the absence of appropriate antiemetic therapy that occurred during the first cycle of the Fol-CHOP therapy.
Once the MTD was established in part 1, an expansion cohort (part 2) applying the MTD was included to allow for better characterization of efficacy and safety. (Figure 1) Patients were treated with the pralatrexate MTD on days 1 and 8 of each 21-day cycle, administered ∼15 minutes after CHOP. Treatment was repeated every 21 days (1 cycle) for up to 6 cycles.

Part 2 treatment schedule: six 21-day cycles.

Patients received prophylaxis with acyclovir and sulfamethoxazole/trimethoprim during the study as well as primary prophylaxis with growth factors (filgrastim or pegfilgrastim) starting in cycle 1 (after the second dose of pralatrexate). All patients were recommended with initiate vitamin supplementation with folic acid and vitamin B12, per the currently approved label. Folic acid (1.0 mg by mouth daily) was initiated at least 10 days before pralatrexate administration. Vitamin B12 (1 mg IM) was administered within 10 weeks before the initiation of pralatrexate and was allowed to be administered during screening. Subsequent vitamin B12 injections were administered the same day as treatment with pralatrexate, and patients received vitamin B12 every 8 to 10 weeks during treatment with pralatrexate.
Patients were instructed to take leucovorin tablets (25 mg) 3 times a day for 2 days beginning 24 hours after each pralatrexate treatment as mucositis prophylaxis.20 The next dose of pralatrexate began at least 72 hours after the last dose of leucovorin administration.
Patients participated in the study for ∼26 weeks, which included a screening period (up to 30 days), up to six 3-week treatment cycles (18 weeks), and an end-of-study visit, which occurred at least 30 days after the last dose of pralatrexate.
Publication 2023
All patients who received ≥1 dose of pralatrexate were evaluable for safety, which was assessed by reported AEs, laboratory assessments, and physical examinations, and graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events scale, version 4.03. AEs were characterized by intensity (severity), causality, and seriousness by the investigator and recorded from the first dose of pralatrexate until at least 30 days after the last dose.
Publication 2023
This multicenter, open-label, dose-finding, dose-escalation phase 1 trial was conducted in 2 parts: the first with the primary objective to evaluate the MTD of pralatrexate in combination with CHOP and the second part with an expansion cohort of 30 patients treated at the MTD to better characterize safety and efficacy of 6 cycles of the pralatrexate-CHOP (Folotyn-CHOP [Fol-CHOP]) combination.
The study was reviewed and approved by the institutional review boards at each of the 4 participating sites and was registered at as NCT02594267. The study conduct complied with the Declaration of Helsinki and followed International Conference on Harmonization Guidelines for Good Clinical Practice. All participating patients provided written informed consent and understood that study participation was voluntary.
Publication 2023

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More about "Pralatrexate"

Pralatrexate, also known as Folotyn, is a folate analog antimetabolite drug used in the treatment of peripheral T-cell lymphoma (PTCL).
It functions by inhibiting the enzyme dihydrofolate reductase (DHFR), which is essential for the synthesis of DNA and cellular proliferation.
The SuperScript II Reverse Transcriptase and PrimeScript RT reagent kit are commonly used in RNA extraction and cDNA synthesis, while the RNeasy Mini Kit and RNAprotect aid in preserving RNA integrity.
The FACSCalibur flow cytometer and TaqMan PCR Master Mix, TaqMan Fast Advanced Master Mix, and TaqMan probes and primers are utilized for cell analysis and gene expression studies, respectively.
DMSO is a common solvent used in various experimental procedures.
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