Bioisosteric Replacements

Bioisosteres - A bioisostere is a molecule resulting from the exchange of an atom or of a group of atoms with an alternative, broadly similar, atom or group of atoms. The objective of a bioisosteric replacement is to create a new molecule with similar biological properties to the parent compound. The bioisosteric replacement may be physicochemically or topologically based. The replacement can attenuate toxicity, modify activity of lead, and/or alter pharmacokinetics or the toxicity of the lead. The order in the table below does not imply any preference, all substituents on a row are often interchangeable. It should be noted that often it is not possible to simply replace one halogen with another, bonds to halogen are significantly weaker than hydrogen bonds and there are significant differences in the nature of the interaction.

Simple replacements

• H D F

• Me NH₂ OH F Cl

• Cl PH₂ SH CN

• Br iPr CF₃

• I tBu CF₃

• CH₂ NH O S

• CO₂R CONHR COSR COCH₂R

• -CH= -N= -S-

• C Si

• Phenyl Pyridyl Thiophene 4-Fluorophenyl

• -OH -F -OMe

• -O- -CF₂-

Replacement of Hydrogen by Deuterium

Perhaps the most conservative is the replacement of hydrogen by deuterium, whilst the change does have a minor impact on the physicochemical properties the change is usually introduced to modulate metabolism. If the bond to the hydrogen being replaced is broken during the rate-determining step, then reduced rate of metabolism might be anticipated based on the kinetic isotope effect. The effect can vary for 1 to 7-fold, dueteration of SDZ-254 reduces the rate of metabolism by 50% in vitro.

Ivacaftor (Kalydeco) is a drug used to treat cystic fibrosis in people with certain mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Ivacaftor is a "potentiator" of CFTR, meaning it increases the probability that the defective channel will be open and allow chloride ions pass through the channel pore. Ivacaftor is extensively metabolised in humans. In vitro and in vivo data indicate that ivacaftor is primarily metabolised by CYP3A to the hydroxy and carboxylate metabolites both of which are much less active. In addition the levels of the metabolites exceed the levels of the parent compound after 8 hours.

The deuterated analogue CTP-656 has similar in vitro activity but metabolism is considerably reduced. In Phase I studies it was shown that CTP-656 C24hr and AUC0-24hr enhanced ~ 3-fold and oral clearance reduced to 1/3 of Ivacaftor. In addition the levels of the metabolites were considerably lower and never exceed the parent drug. Presented at 39th European Cystic Fibrosis Conference June 8-11, 2016.

Tetrabenazine is used for the treatment of Huntington’s Disease–Related Chorea. Tetrabenazine acts primarily as a reversible high-affinity inhibitor of mono-amine uptake into granular vesicles of presynaptic neurons by binding selectively to VMAT-2. Whilst Tetrabenazine is well absorbed it has relatively low bioavailability DOI and the primary route for metabolism is via oxidation by CYP2D6. Deutetrabenazine from Teva, found the half-life of deutetrabenazine is nearly twice that of tetrabenazine, allowing it to be administered twice rather than three times a day, and at lower doses, thus reducing peak concentration adverse effects while maintaining efficacy,

Whilst many of the examples describe the use of deuterium to block cytochrome P450 mediated metabolism it has also been used to modify Aldehyde Oxidase mediated metabolism. The c-Met inhibitor JNJ38877605 has proven effective as an antitumor agent, however clinical studies were terminated due to renal toxicity. It was reported that the renal toxicity was caused by the poor solubility of its aldehyde oxidase (AO) metabolites DOI. Introduction of deuterium reduced the appearance of the AO derived metabolites in vitro and decreased AO metabolites in the plasma as well as 1.88-fold AUC and 1.56-fold Cmax compared with JNJ38877605 in vivo. Moreover, after oral administration to the EBC-1 tumor-bearing nude mice, the deuterated analogue exhibited a better antitumor efficacy than JNJ38877605.

Osimertinib is a highly potent and selective third-generation epidermal growth factor receptor (EGFR) inhibitor, there are two main metabolites AZ7550 and AZ5104. AZ5104, a primary toxic metabolite of osimertinib, has been reported to cause unwanted toxicities. The deuterated analogue Dosimertinib demonstrated robust in vivo antitumor efficacy and favourable PK profiles, but with lower toxicity than Osimertinib DOI.

Deuterium to enhance chemical stability

Some molecules contain a stereocentre that epimerises in vitro and/or in vivo, in these cases replacement of the of the acidic proton with deuterium at the chiral centre of a single stereoisomer might decrease the rate of atom abstraction and afford a good strategy to stabilise chemically unstable stereoisomers.

Telaprevir is an inhibitor of the hepatitis C virus (HCVa) NS3-4A protease, One of the major metabolites of Telaprevir is its P1-(R)-diastereoisomer, containing an inversion at the chiral center next to the α-ketoamide on exchange of a proton with solvent. This compound is approximately 30-fold less active against HCV protease. In an attempt to suppress the epimerization of 2 without losing activity against the HCV protease, the proton at that chiral site was replaced with deuterium (d). The compound 1 (d-telaprevir) is as efficacious as Telaprevir in in vitro inhibition of protease activity and viral replication (replicon) assays. The kinetics of in vitro stability in buffered pH solutions and plasma samples, including human plasma, suggest that d-telaprevir is significantly more stable. Oral administration (10 mg/kg) in rats resulted in a 13% increase of AUC for d-telaprevir DOI.

Replacement of Hydrogen by Fluorine

In an similar replacement of one or more hydrogens by Fluorine has been used to modulate metabolism or off-target activity. Fluorine can be used to modulate the pka of a basic nitrogen, but one has to remember that any advantage can be offset by the resulting increase in LogD. The C-F bond is particularly strong and thus resistant to metabolic cleavage, since fluorine is also highly electron-withdrawing it serves to reduce the potential for oxidative metabolism.

The medchem program leading to the discovery of ezetimibe nicely illustrates the combined use of biosiosteric replacements (H to F and methoxy to F) together with the recognition of active metabolites. Importantly the beneficial effects were seen in multiple species. The discovery of ezetimibe: a view from outside the receptor. J. Med. Chem. 2004, 41, 1–9 DOI: dx.doi.org/10.1021/jm030283g.

The use of Fluorine in drug discovery has been reviewed DOI: 10.2174/156802606777951073, as have the synthetic methodologies available DOI: 10.1021/op700134j

Replacement of Carbon by Silicon

The replacement of carbon by silicon is a relatively recent exploration and whilst this does appear to be a relatively benign conversion it may be the introduction of silicon is to offer potential patent novelty. The anti fungal agent Flusilazole was developed by DuPont, whilst Silafluofen is a pyrethroid insecticide.

Interestingly replacement of a t-butyl group by trimethylsilyl resulted in a significant reduction in LogP for the silicon analogue of BIRB-796 shown below, biological activity and metabolism appeared to be unchanged but in the case of a lipophilic molecule the reduction in LogP may help pharmaceutical properties. DOI: 10.1016/j.bmcl.2006.10.044

t-Butyl bioisostere

The trifluoromethyl oxetane has been evaluated as a tert‐butyl isostere DOI. It was demonstrated that the trifluoromethyl oxetane‐containing had decreased lipophilicity, improved lipophilic efficiency (LipE) and metabolic stability relative to the corresponding tert‐butyl analogue. They were prepared from the corresponding trifluoromethyl ketones.

3,4-Diemethoxyphenyl bioisosteres.

As part of the work towards Orally Available Cathepsin K Inhibitors DOI dx.doi.org/10.1021/jm301119s the Astra Zeneca group prepared the 3,4-dimethoxy compound shown below, whilst this had good exposure in several species in vitro metabolism studies showed formation of glutathione (GSH) adducts after incubation in both rat and human hepatocytes, presumably arising from demethylation followed by oxidation to form a reactive intermediate.

Replacement of methoxy by alkyl resulted in reduced metabolic stability, however 5 or 6 membered rings restored metabolic stability whilst avoiding the possible formation of a reactive metabolite. The indazole had lower plasma protein binding.

Nitro bioisosteres

At the 17th RSC-SCI Medicinal Chemistry Conference in Cambridge Alexander Pasternak (Merck) gave an excellent talk on their work to identify a potent and selective ROM-K inhibitor as novel diuretics. The ROM-K potassium channel is a member of the inward rectifier family of potassium channels expressed in two regions of the kidney: thick ascending loop of Henle and cortical collecting duct DOI, ROMK participates in potassium recycling across the luminal membrane which is critical for the function of the Na+/K+/2C1" co-transporter, the rate- determining step for salt reuptake in this part of the nephron. At the cortical collecting duct , ROMK provides a pathway for potassium secretion that is tightly coupled to sodium uptake through the amiloride sensitive sodium channel. This makes ROM-K an attractive potassium sparing diuretic target.

To cut a long story short Merck ran a HTS campaign (actually I think they ran two) and the only hit is shown below.

As I am sure all medicinal chemists are aware nitro groups, in particular aromatic nitro groups are well known to be reduced in vivo yielding hydroxylamines and nitrosoamines that are highly reactive species and are known carcinogens. So whilst one nitro in the hit is bad imagine how it feels to have two!

The Merck group however followed this lead up and managed to identify several bioisosteric replacements for the nitro group,

I’ve used TorchLite from Cresset to create a view of the electrostatic fields shown below.

Worth reading

Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design DOI

Bioisosteres in Medicinal Chemistry (Methods and Principles in Medicinal Chemistry

Applications of Deuterium in Medicinal Chemistry DOI

SwissBioisostere: a database of molecular replacements for ligand design DOI

There is also SwissBioisostere a web service designed to give ideas about potential bioisosteres, this is derived from a matched molecular pair (MMP) analysis of ChEMBL 17. Two different queries are possible: You are interested in a range of possible replacements for a single substructure ( e.g. replacements for an amide group ); or you want to know details about a particular substructural replacement of interest ( e.g. carboxylic acid vs. tetrazole ). Whilst this is very comprehensive it contains a lot of transformations that were never intended to be bioisosteric replacements.

Last Update 30 January 2021