Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase and the bifunctional dCTP deaminase:dUTPase (DCD:DUT), respectively, were both shown to be expressed in B. halodurans, and both genes were subject to repression by the nucleosides thymidine and deoxycytidine. The latter nucleoside presumably exerts its repression after deamination by cytidine deaminase. Both comEB and dcdB were cloned, overexpressed in Escherichia coli, and purified to homogeneity. Both enzymes were active and displayed the expected regulatory properties: activation by dCTP for dCMP deaminase and dTTP inhibition for both enzymes. Structurally, the B. halodurans enzyme resembled the Mycobacterium tuberculosis enzyme the most. An investigation of sequenced genomes from other species of the genus Bacillus revealed that not only the genome of B. halodurans but also the genomes of Bacillus pseudofirmus, Bacillus thuringiensis, Bacillus hemicellulosilyticus, Bacillus marmarensis, Bacillus cereus, and Bacillus megaterium encode both the dCMP deaminase and the DCD:DUT enzymes. In addition, eight dcdB homologs from Bacillus species within the genus for which the whole genome has not yet been sequenced were registered in the NCBI Entrez database. The biosynthetic route to the nucleotide dUMP, the precursor of dTTP, as shown in Fig. 1, differs between organisms and sets it apart from the rest of nucleotide metabolism (1). This is in agreement with the general belief that uracil was the original DNA base-pairing partner for adenine and that the biosynthesis of dTTP from dUMP arose later in evolution (2). The deoxyribonucleotides dGTP, dATP, and dCTP are all produced in a pathway that goes through the multisubstrate enzyme ribonucleotide reductase. This enzyme is highly regulated in order to maintain the balance of deoxyribonucleotide pools (3-5). dUTP is also formed by ribonucleotide reductase, but because of the toxicity of this nucleotide (6, 7), all organisms express an enzyme with dUTPase activity that hydrolyzes dUTP to dUMP (8).The direct formation of dUMP via ribonucleotide reductase (Fig. 1) is not an efficient process, as the ribonucleotide reductase has a reduced affinity for UDP compared to the affinities of three other canonical ribonucleotides (9-12). Instead, most of the dUMP arises from deamination of cytosine deoxyribonucleotides (13-15). Enteric bacteria synthesize an enzyme with dCTP deaminase activity that converts dCTP into dUTP (EC 3.5.4.13), which accounts for 70 to 80% of the dUMP production (15). The dCTP deaminase is a homotrimeric enzyme structurally related to the trimeric dUTPase and part of the dCTP deaminase/dUTPase superfamily (16-18). The genomes of many Gram-positive bacteria and all eukaryotes encode a dCMP deaminase (EC 3.5.4.12) that shares no resemblance to the enteric dCTP de...
Specifically tailored amino acidebased formulations were previously shown to have a high potential to avoid stress-mediated degradation of complex molecules such as monoclonal antibodies and viral vectors. By using adenovirus 5 (Ad5) as a model, we studied whether such formulations may also efficiently protect viral vectors in thermal stress experiments and during long-term liquid storage. Algorithm-based amino acid preselection using an excipient database and subsequent application of design of experiments (DoE) in combination with a 37 C challenging model enabled the prediction of long-term storage stability of Ad5. By statistical analysis of the Ad5 infectivity, amino acids with significant influence on Ad5 stability were detected after 2 and 3 weeks of liquid storage at 37 C. Ad5 formulations comprising positively selected amino acids did not reveal any loss of infectivity after 24 months in liquid storage at 5 C. By contrast, a 2 log reduction after 3 months and complete loss of infectivity after 18 months was observed with a standard viral vector formulation. By an optimization round, we designed a simple and well-balanced formulation avoiding MgCl 2 , previously considered essential in Ad5 formulations. This work demonstrates the efficacy of an algorithm-based development approach in the formulation development for viral vectors.
To develop highly concentrated therapeutic antibodies enabling convenient subcutaneous application, well stabilizing pharmaceutical formulations with low viscosities are considered to be key. The purpose of this study is to select specific amino acid combinations that reduce and balance aggregation, fragmentation and chemical degradation, and also lower viscosity of highly concentrated liquid antibodies. As a model, the therapeutically well-established antibody trastuzumab (25->200 mg mL ) in liquid formulation is used. Pre-testing of formulations based on a stabilizing and protecting solutions (SPS®) platform is conducted in a thermal unfolding model using differential scanning fluorimetry (DSF) and accelerated aging at 37 and 45 °C. Pre-selected amino acid combinations are further iteratively adjusted to obtain stable highly concentrated antibody formulations with low viscosity. Size exclusion chromatography (SE-HPLC) reveals significantly lower aggregation and fragmentation at specific amino acid:sugar and protein:excipient ratios. Dynamic viscosities <20 mPa * s of highly concentrated trastuzumab (≥200 mg mL ) are measured by falling ball viscosimetry. Moreover, less chemical degradation is found by cationic exchange chromatography (CEX-HPLC) even after 6 months liquid storage at 25 °C. In conclusion, specifically tailored and advanced amino acid-based liquid formulations avoid aggregation and enable the development of stable and low viscous highly concentrated biopharmaceuticals.
Background:With both the approvals of CD19 CAR‐T cell therapies and promising clinical data of gene therapy trials such as in hemophilia or sickle cell disease, recent years have seen significant progress of gene and cell therapy in the field of hematological malignancies as well as rare hematologic genetic disorders. Hence, replication‐deficient recombinant viral vectors such as adenovirus serotype 5, adeno‐associated virus and members of the poxvirus family represent a rapidly growing field of vaccine development and gene therapy.Viral vectors are known as complex supra‐molecular ensembles of macromolecules produced by living organisms (nucleic acids, proteins, polysaccharides and in the case of lipid enveloped viruses of phospholipids) which are prone to a variety of complex chemical and physical degradation pathways, in particular due to stress induced by manufacturing, storage and distribution. This represents a significant hurdle for the development of stable vector‐based pharmaceuticals such as vaccines or gene therapeuticsAims:Here, we studied whether LEUKOCAREs formulation platform may also efficiently protect viral vectors in thermal stress experiments. As a representative example of viral vectors we used adenovirus serotype 5 (Ad5).Methods:In an algorithm‐based development approach, we used Design of Experiment (DoE) to select the most effectively stabilizing formulations for Ad5. We stored Ad5 at 37 °C and 25 °C as accelerated aging temperature to identify the most effective stabilizing excipients after short term storage as well as at 5 °C for real time storage. Based on these results, the best selected formulations were further iteratively optimized and used in long term storage at 5 °C.Results:By analysis of the infectious virus titers and mathematical combination of these results with the DoE matrix, the linear influence of each amino acid used in the DoE matrix was determined. The accelerated aging conditions were shown to be predictive for real‐time aging. Several of the excipients indicated a neutral influence, whereby we observed the importance of a well‐balanced combination of the components with each other regarding concentration and stabilizing interactions. The predictive potential of this approach was confirmed by two iteratively composed formulations tailored for Ad5 during long‐term storage.Summary/Conclusion:The pre‐selection strategy of effectively stabilizing excipients by means of an algorithm‐based development approach and the applied accelerated aging model is highly efficient and enables the generation of best‐in‐class stability formulations for Ad5 viruses and viral vectors in liquid. Moreover, this approach could have beneficial impact when applied early in downstream processing, which could enable significant reduction of viral vectors manufacturing costs for gene therapy.
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