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Biosynthetic pathways to produce pharmaceuticals over large-scale benchtop chemistry.

Biosynthetic pathways to produce pharmaceuticals over large-scale benchtop chemistry.

Question 1:

What is one motivation to use biosynthetic pathways to produce pharmaceuticals over large-scale benchtop chemistry?

Question 2:
Given the process diagram shown in supplemental figure 1, name 2 steps that can be taken to maximize ethanol production over all other products (succinate, formate, etc.). Assume you are working in a highly controlled bioreactor and that you have access to any of the molecules used in the process. Keep in mind that ethanol biosynthesis takes place under anaerobic conditions.

Question 3:

Given a glucose input of 50 kg, what is the maximum theoretical output of ethanol, assuming you have optimally controlled the above reaction and the only product is ethanol. Give your answer in kg of ethanol, and round to two decimal places.

Man-made biology (SB) is surely an promising self-control, which can be slowly reorienting the industry of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell–cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.

The newest area of man-made biology (SB) is arguably reorienting the industry of medicine discovery (DD) in a similar manner as one century ago the field of organic chemistry was at the core of creativity in the pharmaceutical drug sectors. Today, the increasing drug attrition rate, with 95% of drugs tested in Phase I not reaching approval,1 testifies the difficulty to innovate for safe medicines with the current approaches of medicinal chemistry.

SB brings the engineer’s perspective into biology, which transforms a biological cell into a commercial biofactory. Nature has been the source of human medicines for thousands of years, but the difficulty of large-scale production of natural products (NPs) made pharmaceutical industries to abandon this source of natural medicinal compounds. As such, their therapeutic advantages (eg, biocompatibility) were sacrificed to turn toward simpler chemistry at the risk of increased cross-reactivity with secondary therapeutic targets and even unwanted off-targets as confirmed by recent studies in system chemical biology.2–4 Such target promiscuity is often responsible for observed toxicity issues that can jeopardize a project at clinical stage.5

A breakthrough finding from the 1990s produced the rational-based hereditary design and style a potential strategy for DD. Microorganisms (as well as plants and others) produce secondary metabolites using gigantic biosynthetic units.6 These enzymatic modules can be manipulated in combinatorial fashion in synthetic cells to produce new NPs derivatives.7 The first application of SB in DD was to boost innovation in creating new chemical scaffolds that have properties similar to well-known NP-derived human medicines, increasing the chance of being bioactive with the right pharmacological properties.

The initial portion of this overview offers a summary of the basic notion of SB followed by an historic advancement of the methods employed in pharmaceutical research and just how the application of SB in DD naturally come about from present day poly-pharmacology. The third section presents the impact of SB in the field of NPs. The fourth section shows the latest development of metabolic engineering in the large-scale production of drugs by microorganisms. Synthetic cellular models can be constructed to identify or validate drug target (fifth section) as well as to create target-based or phenotypic-based drug screening platform (sixth section).11–15 The following section describes the construction of disease models with the help of optogenetics to decipher disease mechanisms with examples in cancer and neuronal diseases. Finally, the last two sections discuss some other challenging topics in DD, such as toxicity and drug resistance.

One hundred yrs ago, Paul Ehrlich introduced the concept of “One medication – One Focus on – One disease” where a medication would heal a condition by focusing on a unique aspect of our system.18 These kinds of “magic bullet” was to be found in general through pharmacologically lively ingredients obtained from plants or organisms. “Tour de force” was achieved by chemists to reproduce these molecules by total synthesis.19 New cost-effective approaches such as function-oriented synthesis emerged in order to mimic complex NPs with simpler products while retaining similar pharmacophore pattern of interactions. NPs and NPs biomimetism marked the golden age of chemistry and established the success of the pharmaceutical industries for the next century.20

A culminant period of time was observed at the convert of your previous century with the developments in sound- and fluid-period syntheses. Combinatorial chemistry opened the possibility of exploring unknown regions of the chemical space by systematic decoration of predefined chemical scaffolds.21,22 Together with the miniaturization of biochemical assays, large-scale chemical libraries could be screened for binding affinity with a chosen biological target.23 Before validating the proof of success of this approach, pharmaceutical industries abandoned most of their research programs on NPs and bet on the high-throughput screening (HTS) approach to find initial hits for the therapeutic target under investigation.24

Accomplishment with this technique would depend heavily on the caliber of the enter ingredient libraries. To increase the chance of success, selection of compound libraries was based on chemical diversity and optimization of physicochemical properties (eg, solubility and permeability). With the addition of structural knowledge on the target, new constraints were included in the optimization process to produce target-focused compound libraries that are specifically designed for a selected set of targets.25

This improves one other issue of substance specificity, for instance, its capacity to combine an exclusive biological objective.26 Cross-reactivity with structurally similar and unwanted biological concentrates on would induce toxicity. This usually arises when targeting a specific member of a large protein family (eg, kinases). To control the selectivity of drug candidates, industries and academic structural genomics research centers developed high-throughput biochemical assay platforms to screen compounds’ libraries on a representative set of a protein target family members (eg, kinases27). This approach led to the accumulation of chemical proteomics data that showed that even selective compounds bind to more than one biological target.28,29 In that way, the systemic view of pharmacology has moved the Paul Ehrlich’s concept (“single drug – single target”) toward a more subtle point of view involving interactions with multiple targets (poly-pharmacology) which are modulated by synergistic drug combinations.30–33

SB is really a realistic try to understand the basic concepts on this obvious complexness. Using an engineer’s view in biology, SB designs biological devices (synthetic cells or cell-free system) to trigger a biological response with respect to input controlled signal (Figure 1). In DD, such devices would be used to activate gene expression of biosynthetic units to explore NP-like chemical space. In-cell synthesis has the advantage to make use of natural evolution to create compounds compliant to biological environment, which is part of the lead optimization process. Genome editing tools give the possibility of following through reporter genes the action of a particular output signal, which is very useful to validate drug target or disease models as well as merging constraints from both DD and drug production. This “rational-based biosynthetic drug design”34 approach is somehow the other side of the de novo rational-based drug design of the last century.