Multi-objective optimization of glycopeptide antibiotic production in batch and fed batch processes

High cell density cultivation of E. coli in shake flasks for the production of recombinant proteins

•

True fed-batch strategy for high cell density cultivation of E. coli in shake flask.

•

Cybernetic model-based optimization of the feeding recipe.

•

Biomass of 19.9–21.5 g DCW/L, in agreement with the model prediction.

•

Volumetric productivity for tested proteins increased 8–34-fold compared to batch.

•

Scale up of fed-batch recipe to bioreactor resulted in further 2.8-fold increase.

Batch cultivation of recombinant bacteria in shake flasks typically results in low cell density due to nutrient depletion. Previous studies on high cell density cultivation in shake flasks have relied mainly on controlled release mechanisms. Here, we report a true fed-batch strategy to achieve high cell density of recombinant E. coli in shake flasks in 24 h by feeding a mixture of glycerol and yeast extract with a syringe pump. Feed composition and feed rate were obtained by cybernetic model-based, multi-objective optimization. Model parameters were estimated from time-course measurement of substrate, biomass, and dissolved oxygen levels. The optimized process yielded 20.7 g dry cell weight/L, in agreement with the model prediction. Volumetric protein productivity improved by 10–34-fold compared to batch cultivation with 2.8-fold further improvement when the fed-batch process was replicated in a 3 L bioreactor. The process has significance in the routine laboratory cultivations and in scaleup studies.

In-Situ Recovery of Persipeptides from Streptomyces zagrosensis Fermentation Broth by Enhanced Adsorption

Background:

Drug discovery process is growing considerably due to the noteworthy resource of natural products. Persipeptides A and B are cyclopeptide antibiotics, which are produced by Streptomyces zagrosensis UTMC 1154. Although extraction of culture broth with the help of solvent has been optimized previously, no effort for In-Situ extraction of persipeptides has been done yet.

Objective:

To produce a high quantity of persipeptides for further drug evaluation, it is crucial to design approaches aimed at improvement of the extraction yield.

Materials and Methods:

Amberlite XAD-16N was employed into the fermentation culture medium of S. zagrosensis in order to enhance the In-Situ extraction of persipeptides. Effects of resin content (%), resin addition time (h), and fermentation time (day) were investigated by a two-level full factorial experimental design.

Results:

The main factors of resin content (%) and the interaction of resin content (%) with resin addition time (day) were found to be important using ANOVA. The results showed the amount of 0.33 % (w.v^-1) amberlite XAD-16N added at 27.2 h post-inoculation was the most effective combination to increase the efficiency of In-Situ adsorption capacity of persipeptides.

Conclusions:

The provided method requires 3.3 g resin and 200 mL methanol for the extraction of persipeptides from each liter of fermentation culture of S. zagrosensis in less than 15 min. Apart from cost-efficiently and simplicity, this procedure enhanced the recovery of persipeptides by 7 % and 3 times, compared to ISP2 medium without any resin after 4 and 7 days of fermentation, respectively. Therefore, this method can be regarded as a cost-efficient enhancement approach for the production of these newly-discovered metabolites before implementing the genetic manipulation or intensive media optimization, demanding considerable time and effort.

Multi-objective optimization methods in novel drug design

Introduction: In multi-objective drug design, optimization gains importance, being upgraded to a discipline that attracts its own research. Current strategies are broadly classified into single - objective optimization (SOO) and multi-objective optimization (MOO).Areas covered: Starting with SOO and the ways used to incorporate multiple criteria into it, the present review focuses on MOO techniques, their comparison, advantages, and restrictions. Pareto analysis and the concept of dominance stand in the core of MOO. The Pareto front, Pareto ranking, and limitations of Pareto-based methods, due to high dimensions and data uncertainty, are outlined. Desirability functions and the weighted sum approaches are described as stand-alone techniques to transform the MOO problem to SOO or in combination with pareto analysis and evolutionary algorithms. Representative applications in different drug research areas are also discussed.Expert opinion: Despite their limitations, the use of combined MOO techniques, as well as being complementary to SOO or in conjunction with artificial intelligence, contributes dramatically to efficient drug design, assisting decisions and increasing success probabilities. For multi-target drug design, optimization is supported by network approaches, while applicability of MOO to other fields like drug technology or biological complexity opens new perspectives in the interrelated fields of medicinal chemistry and molecular biology.

Model based optimization of high cell density cultivation of nitrogen-fixing cyanobacteria

In the present study, fed-batch cultivation of Cyanothece sp. ATCC 51142, a known hydrogen producer, was optimized for maximizing biomass production. Decline in growth of this organism in dense cultures was attributed to increased substrate consumption for maintenance and respiration, and photolimitation due to self shading. A model incorporating these aspects was developed, and by using control vector parameterization (CVP), substrate feeding recipe was optimized to achieve 12-fold higher biomass concentration. The optimization results were verified experimentally on shake flask and bioreactor. The latter resulted in greater exponential growth rate possibly by overcoming photolimitation by simulating flashing light effect. Such a strategy can be readily applied for mixotrophic cultivation of cyanobacterial cultures in the first stage followed by photoautotrophic growth at the production stage.

Metabolic flexibility of d-ribose producer strain of Bacillus pumilus under environmental perturbations

The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the d-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of d-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for d-ribose producers conducted in the 1970s.