What We Do

Late-stage Functionalisation

Late-Stage Functionalisation

Late-stage oxidised derivatives of drugs by biotransformation

Multiple oxidised derivatives of drug leads can be accessed in parallel using Hypha’s PolyCYPs® enzymes. PolyCYPs enzymes are cloned from some of Hypha’s microbes talented at oxidising drugs, and provide a mechanism to quickly screen lead compounds for hydroxylated and other oxidised derivatives.

PolyCYPs enzymes are available in kit form to allow reactions to be performed in client labs with the option of either a 20-enzyme screening kit (18 PolyCYPs, AOX and FMO3) or 8-enzyme (8 promiscuous PolyCYPs) diversification kit.

Hypha can also undertake screening of drug compounds using PolyCYPs through a service option called PolarExplorer. We operate this as a flexible end-to-end package which includes screening, scale-up, purification and optional structure elucidation of derivatives.

Why bother with late-stage hydroxylation?

Biotransformation of drugs has led to intriguing findings. In particular, oxidation of drug leads by hydroxylation, subsequent oxidation to carboxyls, or dealkylation can lead to derivatives that have superior properties to the parent molecule. These derivatives may or may not be the major metabolites observed in the in vitro / in vivo system, as sometimes the minor metabolites or derivatives that might otherwise be overlooked, or not made in the specific in vitro system employed, may possess the improved properties.

Late-stage hydroxylation is a key tactic highlighted in a paper by Bostrom et al. in which examples of Hypha’s biotransformation technology were featured. The paper describes the potential benefits of hydroxylation, as part of a toolkit for medicinal chemists, which can result in improved activity, selectivity, solubility, and lipophilicity through replacing or mimicking water in binding site interactions.

Addition of a hydroxyl group can also influence pharmacokinetic (PK) properties as illustrated in the work by Stepan et al. where a PDE2 (phosphodiesterase 2) inhibitor lead compound at Pfizer suffered from exclusive clearance by CYP3A4. Through biotransformation profiling of the parent compound, several hydroxylated derivatives were produced, all of which maintained potency and also possessed higher metabolic stability. Whole cell biotransformation was used to produce hundreds of milligrams of one of these hydroxylated derivatives for ADME characterization using a streptomycete bacterium, a process subsequently able to be replaced by an 8-step chemical synthesis in order to provide multi-gram amounts for in vivo studies. The hydroxylated lead candidate was found to possess exquisite drug-like properties including a low oxidative turnover, increased renal excretion, and good selectivity against other phosphodiesterases.

Potential benefits of late-stage hydroxylation

Identify metabolites and CYP enzyme soft spots

Improve DMPK properties

Expand SAR understanding and exemplify active metabolites in patents

Probe for beneficial polar interactions

Enhance potency or selectivity

Case Studies

Late-stage hydroxylation of a drug lead to improve LLE

Introduction of a hydroxyl group at the tert-butyl position of a Gilead kinase inhibitor using Hypha’s biocatalysis technology resulted in not only increased polarity but also an unanticipated 20-fold boost in potency such that the ligand-lipophilicity efficiency (LLE) was increased by 2.6 units to a more drug-like 6.0. This oxidised derivative was not a compound that would ordinarily have been synthesized, thus biotransformation provided an unexpected and valuable insight.

Late-stage hydroxylation of a drug lead for exploration of SAR

In this case study, five active monohydroxylated derivatives of a big pharma client’s drug lead were produced using PolyCYPs, with a 56% conversion of the parent drug by the best PolyCYP enzyme, enabling access to polar chemical space in parallel as part of SAR studies.

Gilead lle structures


Explore our library of resources comprising brochures, case studies, posters and publications about the work we do.

Introducing oxygen into a drug candidate late in the optimisation process has several applications including exploration of SAR (structure-activity relationships) and the ability to access derivatives that may possess superior properties such as improved metabolic stability and LLE (ligand-lipophilicity efficiency). Biocatalysis can provide access to chemical space in a complementary manner to chemical synthesis and provide a “one-experiment” solution to accessing multiple derivatives in parallel. This poster illustrates the application of a new biocatalysis kit, PolyCYPs®, to enable parallel synthesis of hydroxylated derivatives of drugs.

The first-in-class JAK inhibitor, ruxolitinib (trade names Jakafi® and Jakavi®), is primarily metabolized to a complex mixture of stereoisomeric cyclopentyl hydroxyl and keto metabolites. Application of Hypha’s microbial-based biocatalytic C-H bond activation to ruxolitinib resulted in the production of an array of hydroxylated and further oxidized keto metabolites, many of which corresponded to circulating human metabolites. All possible oxidized isomers of the aliphatic cyclopentyl moiety were derived from a variety of microbial species which were readily scaled up, enabling efficient production of stereoisomer metabolite standards for structural characterization and bioanalytical monitoring.

In this paper, authors from Hypha and Incyte Corporation discuss the impact and application of biotransformation of drugs by mammalian systems, microorganisms, and recombinant enzymes, covering active and reactive metabolites, the impact of the gut microbiome on metabolism, and how insights gained from biotransformation studies can influence drug design.

Test tubes with dripper
251A3171-DE01-48EB-AA27-BD82BC5AC10DCreated with sketchtool.

We would like to mention that it has been a pleasure to work with Hypha in this project. We are really satisfied with how the collaboration has progressed, reaching the defined goals and timelines in a very efficient manner. Access of hydroxylated compounds through PolyCYPs has saved our company time and resources. We are sure that we will have more opportunities to work together in the future.

Program Leader

European Pharma Company

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