Dynamic metabolic network modeling of mammalian Chinese hamster ovary (CHO) cell cultures with continuous phase kinetics transitions

Abstract

Cellular biological environments are difficult to analyse on the first principle basis. In this modeling work, a novel approach is presented which transits from a broad mechanistic description of the individual metabolic pathways to a simplified macro-kinetic model. The latter is characterized within the concept of metabolic flux analysis and associated elementary modes, which obey the constraints of phenotype. Unlike the piecewise-defined kinetic expressions with a discrete separate treatment of different cell phases, the Monod equation rate law is extended herein, allowing for a dynamic reversal of macro-reactions, and thus, a uniform continuous functionality from growth to death cultivation periods. The enzymatic biochemical reactions of complete metabolic network are defined to satisfy the composition of mammalian culture structure which reflects on stoichiometry. This affords us an opportunity to handle the density of the viable cells (biomass) along with central metabolisms’ transformations, rather than as a decoupled constituent function, as habitually assumed in the literature. The methodology of the extracellular metabolite measurements for the Chinese hamster ovary (CHO) cells is confronted, confirming the applicability in multi-scale biologically-relevant systems. Temporal species’ behavior reveals inflection points that switch among stages. In further extensions metabolic models have a potential to forecast the outcomes of growth medium perturbations, feeding protocols, and process parameters in order to facilitate the productivity and quality of biosimilars in biotechnology.