Bioisosteres Hiroyuki Kobayashi Jan.31.2013 Today, I’d like to talk about bioisosteres This is one of the most fundamental concepts in medicinal chemistry. Jan.31.2013 Hiroyuki Kobayashi

An example of bioisosteres Aminopyrine Marketed as an analgesic and anti-inflammatory drug in 1896. In 1922, It was revealed that Aminopyrine was a carcinogen ! Propylphenazone Developed by Roche in 1951. Bioisosteric modification of dimethylamino group removed its carcinogenic action. First, I’ll show you an example of bioisosteres. One of the most classical drugs, aminopyrine, was marketed as an analgesic and anti-inflammatory drug in 1896. In 1922, it was revealed that Aminopyrine was a carcinogen, however, this drug was used until the 1970s. Then propylphenazone was developed by Roche in 1951. They modified the dimethylamino group of aminopyrine into a isopropyl group to remove its carcinogenic action. This compound is widely used even now. 2

What is bioisostere? Bioisosteres are substituents or groups with similar physical or chemical properties which produce broadly similar biological properties in a chemical compound. Here, I’ll show you the definition of bioisosteres. Bioisosteres are substituents or groups with similar physical or chemical properties which produce broadly similar biological properties in a chemical compound. 3

What is bioisostere? Bioisosteres are substituents or groups with similar physical or chemical properties which produce broadly similar biological properties in a chemical compound. In drug design, the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of 　　　　　　　a compound without making significant changes in chemical structure. In drug design, the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of a compound without making significant changes in chemical structure. 4

The utility of bioisosteres The development and application of bioisosteres have been adopted as a fundamental tactical approach useful to address a number of aspects associated with the design and development of drug candidates. In the contemporary practice of medicinal chemistry, the development and application of bioisosteres has been adopted as a fundamental tactical approach useful to address a number of aspects associated with the design and development of drug candidates. 5

The utility of bioisosteres The development and application of bioisosteres have been adopted as a fundamental tactical approach useful to address a number of aspects associated with the design and development of drug candidates. The utility of bioisosteres is extending to Improving potency Enhancing selectivity Altering physical properties Reducing or redirecting metabolism Eliminating or modifying toxicophores Acquiring novel intellectual property The utility of bioisosteres is extending to Improving potency Enhancing selectivity Altering physical properties Reducing or redirecting metabolism Eliminating or modifying toxicophores Acquiring novel intellectual property 6

Classical bioisosteres Classical bioisosteres represent the result of an early appreciation of the concept and encompass structurally simple atoms or groups Bioisosteres have been classified into classical and non-classical bioisosteres. Classical bioisosteres represent the result of an early appreciation of the concept and encompass structurally simple, mono-,di, and trivalent atoms or groups and a ring equivalent that are shown in this box. 7

Nonclassical bioisosteres Nonclassical bioisosteres are structurally distinct, usually comprised of different number of atoms and exhibit different steric and electronic properties. In contrast, non-classical bioisosteres are structurally distinct, usually comprised of different number of atoms and exhibit different steric and electronic properties. Non-classical bioisosteres have been divided into two subgroups, No.1 Cyclic and non cyclic isosteres Diethylstilbestrol is a non cyclic and non steroidal compound but it has similar activity as a female hormone. No.2 Exchangeable group isosterism in which the properties of discrete functional elements are emulated. Carboxylic acid can be changed into other acidic groups such as tetrazole and acylsulfoneamide. 8

Application of bioisosteres in drug design Next, I’d like to move on to the application of bioisotsteres in drug design.

F as an isostere of H The unique properties of F have led to its widespread application in drug design as an isostere for H, since incorporation of F can productively modulate a range of properties of interest to medicinal chemists. This is the most famous topic of bioisoteres. The unique properties of fluorine have led to its widespread application in drug design as an isostere for hydrogen, since incorporation of fluorine can productively modulate a range of properties of interest to medicinal chemists. Next, I’ll give you some concrete examples. 20% of all drugs are fluorinated compound! 10

F as an isostere of H Improving metabolic stability J. Med. Chem. 2004, 41, 1 (Bayer) Improving metabolic stability One of the strategies to counter low metabolic stability is to block the metabolically liable site with a F substituent and hope that the small F atom will not impair the binding of the target protein. One of the strategies to counter low metabolic stability is to block the metabolically liable site with a fluorine substituent and hope that the small fluorine atom will not impair the binding of the target protein. In Cholesterol absorption inhibitor, the introduction of two fluorine atoms into this lead compound was a critical step toward increased metabolic stability, ultimately optimized in the context of Ezetimb 11

F as an isostere of H Effect on the pKa As the most electronegative atom, F has a very strong effect on acidity or basicity of nearby functional groups. As the most electronegative atom, fluorine has a very strong effect on acidity or basicity of nearby functional groups. Here, you can see the pKa of ethylamine and acetic acid. The more fluorine this amine has, the more its basicity is reduced, while the more fluorine this acid has, the more its acidity is increased. 12

F as an isostere of H Effect on the pKa J. Med. Chem. 2008, 51, 4239 (Merck) Effect on the pKa As the most electronegative atom, F has a very strong effect on acidity or basicity of nearby functional groups. The strategic deployment of a fluorine atom to modulate basicity is probed in the context of Kinesin spindle protein inhibitor. This lead compound has good efficacy but is excreted by p-glycoprotein in the tumor cell because of its basicity. To validate the piperidine unit focused on those reducing basicity, they found that deploying the fluorine substituent in this position reduced bacisity from pKa=8.8 to 7.6.This compound, MK-0731 was subsequently advanced into clinical trials. 13

F as an isostere of H Effect on molecular conformation Bioorg. Med. Chem. Lett. 2010, 20, 2572 (Merck) Effect on molecular conformation As a consequence of the high electronegativity of F, the C-F bond is most polarized and can influence conformational bias via intramolecular electrostatic interactions As a consequence of the high electronegativity of fluorine, the C-F bond is most polarized and can influence conformational bias via intramolecular electrostatic interactions. In CGRP receptor antagonist, substitution of fluorine on the aryl group at the positions ortho to the amide linker was predicted to bias one of two possible planar conformations as shown here. They suggested the bioactive conformation with respect to the central amide was the one depicted for this right structure. 14

D as an isostere of H Substituting a H atom by D represents the most conservative example of bioisosterism given the similarities between the two isotopes, but there are circumstances in drug design where this change can offer a significant advantage. Substituting a hydrogen atom by deuterium represents the most conservative example of bioisosterism given the similarities between the two isotopes, but there are circumstances in drug design where this change can offer a significant advantage. 15

D as an isostere of H D substitution to modulate metabolism Nature 2009, 458, 269 (Concert) D substitution to modulate metabolism The strategic deployment of D at sites of metabolism where H atom abstraction can disturb metabolism and redirect the metabolic pathway. First case of deuterium is ‘Deuterium substitution to modulate metabolism’. The strategic deployment of deuterium at sites of metabolism where hydrogen atom abstraction can disturb metabolism and redirect the metabolic pathway. Paroxetine was sold as an antidepressant by GSK in 1992, This compound is widely used even now but it has side effects caused by inactivation of CYP2D6. The deuterium compound developed by the pharma venture, Concert, relieves the mechanism based inhibition of CYP2D6 associated with the methylenedioxy moiety. 16

D as an isostere of H D to slow epimerization J. Med. Chem. 2009, 52, 7993 (Vertex) D to slow epimerization Deuteration at the labile center shows increased stability toward racemization. Deuteration at the labile center shows increased stability toward recemization. An interesting application of the deuterium isotope has been described for the HCV NS3 protease inhibitor, Telaprevir. The (S)-form a-ketoamide is readily racemized in human plasma to afford the (R)-diasteromer, which exhibits thirty-fold weaker biological activity. This deuteration analog showed increased stability toward racemization. In human plasma, this compound produced only 10% of epimer over 1 hr compared to 35% for protio compound, and the effect translated into a 13% increase in the AUC. 17

Carboxylic acid isosteres Isosteres of carboxylic acid have been studied extensively. These studies have typically focused on Enhancing potency Reducing polarity Increasing lipophilicity (improve membrane permeability) Enhancing pharmacokinetic properties Reducing the potential for toxicity Isosteres of carboxylic acid have been studied extensively. These studies have typically focused on Enhancing potency Reducing polarity Increasing Lipophilicity (improve membrane pereability) Enhancing pharmacokinetic properties Reducing the potential for toxicity 18

Carboxylic acid isosteres Synopsis of carboxylic acid isosteres Common isosteres Heterocycle based isosteres Carboxylic acid bioisostere has been divided into common and heterocycle based isosteres. My favorite isosteres are shown in the blue box. 19

Carboxylic acid isosteres Pharm. Biotechnol. 1998, 11, 29 (DuPont) COOH isosteres in Angiotensin II receptor antagonists Angiotensin II receptor antagonists provide instructive insight into carboxylic acid isostere design, since binding affinity to receptor in a series of biphenyl acids is quite sensitive to the identity of the acidic element. Angiotensin II receptor antagonists provide instructive insight into carboxylic acid isostere design, since binding affinity to receptor in a series of biphenyl acids is quite sensitive to the identity of the acidic element. This sulfonamide moiety confers a 3-fold increase in potency compared to the carboxylic acid analog. Furthermore, the efficacy of the squaric acid analog and the tetrazole analog is superior to both the carboxylic acid and the sulfonamide. Although the efficacy of squarate was lower than the tetrazole analog,this squarate reduced blood pressure in hypertensive rats following oral administration. 20

Carboxylic acid isosteres J. Med. Chem. 2004, 47, 2706 (Aristotle Univ.) 2,6-Difluorophenol as a COOH mimetic The introduction of fluorine atoms the 2- and 6-positions of phenol increase the acidity, prompting the hypothesis that this functionality may function as a lipophilic COOH mimetic. The introduction of fluorine atoms the 2 and 6 positions of phenol increase the acidity, prompting the hypothesis that this functionality may function as a lipophilic carboxyl acid mimetic. The concept of an isosteric relationship was based on a combination of the acidity of the hydroxyl group and the potential for fluorine to mimic the carboxylic acid carbonyl bond by acting as a hydrogen bond acceptor. In aldose reductase inhibitors, the 2,6-difluoropenol moiety was examined as an isostere of the carboxylic acid with the result that this compound offered 6-fold increased potency. 21

Amide and ester isosteres Amide isosteres have typically been of interest as a means of modulating polarity and bioavailability, while ester isosteres have frequently been developed to address metabolism issues since esters can be rapidly cleaved in vivo. Amide isosteres have typically been of interest as a means of modulating polarity and bioavailability, while ester isosteres have frequently been developed to address metabolism issues since esters can be rapidly cleaved in vivo. 22

Amide and ester isosteres Amide isosteres have typically been of interest as a means of modulating polarity and bioavailability, while ester isosteres have frequently been developed to address metabolism issues since esters can be rapidly cleaved in vivo. Synopsis of amide and ester isosteres Here, you can see the synopsis of amide and ester isosteres. My first choices are these heterocycles. 23

Amide and ester isosteres Trifluoroethylamines as amide isosteres The trifluoroethylamine can act as an isostere of an amide moiety in peptide-based molecules. A case of amide isosteres is Trifluoroethylamines as amide isosteres. The trifluoroethylamine can act as isostere of an amide moiety in peptide-based molecules. 24

Amide and ester isosteres Trifluoroethylamines as amide isosteres The trifluoroethylamine can act as an isostere of an amide moiety in peptide-based molecules. Functional mimicry is based on Functional mimicry is based on Reducing the basicity of the amine without compromising the ability of the NH to function as a hydrogen bond donor This bond is close to 120 degrees observed with an amide C-CF3 bond is as polar as CO bond Reducing the bascity of the amine without compromising the ability of the NH to function as a H-bond donor CF3CH(R)NHR’ bond is close to 120o observed with an amide C-CF3 bond is as polar as C=O bond 25

Amide and ester isosteres Bioorg. Med. Chem. Lett. 2008, 18, 923 (Merck) Trifluoroethylamines in Cathepsin K inhibitors . The trifluoroethylamine is an excellent surrogate for amide bond in the inhibitor of Cathepsin K. The trifluoroethylamine is an excellent surrogate for amide bond in the inhibitor of Cathepsin K. The amide moeity of this lead compound was replaced by a trifluoroethylamine, resulting in improved selectivity against cathepsin B and improved metabolic stability but poorer pharmacokinetics properties. Odanacatib was the product of further refinement that solved poor pharmacokinetics properties. This compound is currently in Phase 3 clinical trials. 26

Phenyl ring isosteres Phenyl ring can often be replaced by a heteroaromatic ring or a saturated ring which may improve efficacy, lipophilicity and specificity of binding. Phenyl ring can often be replaced by a heteroaromatic ring or a saturated ring which may improve efficacy, lipophilicity and specificity of binding. 27

Phenyl ring isosteres N substitution for CH in Phenyl ring J. Med. Chem. 2009, 52, 7778 (Bristol-Myers Squibb) N substitution for CH in Phenyl ring The introduction of a pyridine ring was probed systematically with the objective of reducing metabolism of the phenyl ring and toxicity of metabolites. The introduction of a pyridine ring was probed systematically with the objective of reducing metabolism of the phenyl ring and toxicity of metabolites. In HIV-1 attachment inhibitor, the 4,7-dimethoxy substituted indole is a highly potent antiviral compound that is metabolized in vivo, leading to the potential for quinone formation, a known toxicophore. Then 6-aza analog offered improved aqueous solubility and abolished the potential for reactive quinone formation should demethylation occur, which in this series would afford the nontoxic amide. 28

Phenyl ring isosteres Cyclopropane as phenyl isosteres Bioorg. Med. Chem. Lett. 2008, 18, 4118 (Bristol-Myers Squibb) Cyclopropane as phenyl isosteres Cyclopropane was explored as mimetic of the phenyl ring in an effort to identify compounds with reduced molecular weight and a lower lipophilicity. Cyclopropane was explored as mimetic of the phenyl ring in an effort to identify compounds with reduced molecular weight and lower lipophilicity. In FXa inhibitor, the cyclopentane analog demonstrated lower lipophilicity and markedly improved potency compared to the biphenyl analog. Quantum mechanical calculation supported that the phenylcyclopropanes exist in the perpendicular conformation. This perpendicular conformation mimics the biologically active conformation of the ortho-substituted biphenyl moieties. Quantum calculation of biphenyl and phenylcyclopropyl moieties 29

Phenyl ring isosteres Bicyclo[1.1.1]pentane as phenyl isosteres J. Med. Chem. 2012, 55, 3414 (Pfizer) Bicyclo[1.1.1]pentane as phenyl isosteres The bicyclo[1.1.1]pentane motif is ideally suited to dispose two substituents in the required coplanar orientation like p-Ph ring. The bicylco[1.1.1]pentane motif is ideally suited to dispose two substituents in the required coplanar orientation like para-substituted phenyl ring. In the gamma-secretase inhibitor, replacement of the central phenyl ring with the bicyclo[1.1.1]pentane motif led to the discovery of an equipotent inhibitor with significant improvements in permeability and aqueous solubility. This bicyclo[1.1.1]pentane and para-substituted phenyl ring include comparable dihedral angles and similar distances between substituents. Bicyclo[1.1.1]pentane and Ph ring include comparable dihedral angles and similar distances between substituents 30

Phosphate isosteres Phosphate play a central role in cellular signaling and consequently are of great interest to medicinal chemists. However the design of molecules that can interfere with phosphate-based processes is recognized as a significant challenge, especially when the resulting compounds must show good cellular penetration and stability. The last topic is phosphate isosteres Phosphates play a central role in cellular signaling and consequently are of great interest to medicinal chemists. However the design of molecules that can interfere with phosphate based processes is recognized as a significant challenge, especially when the resulting compounds must show good cellular penetration and stability. 31

Phosphate isosteres Difluorophosphonate as phosphate isostere Chem. Comm. 1998, 1087 (Liverpool Univ.) Difluorophosphonate as phosphate isostere Structural and electronic studies have firmly established the fluorinated phosphonates as closely related, hydrolytically and enzymatically stable mimics of the phosphate. Structural and electronic studies have firmly established the fluorinated phosphonates as closely related, hydrolytically and enzymatically stable mimics of phosphate. As shown in the left box, the pKa2 as well as the bond angles obtained from X-ray crystallography clearly indicated the closer analogy between phosphate and difluorophosphonate. In the HIV reverse transcriptase inhibitor, the efficacies of diphosphate and bisphosphonates were examined. These bisphosphonates showed an expected correlation of increase activity with an increase in fluoro-substitution, culminating in the CF2 analog being just an order of magnitude less active than the lead compound. In human blood serum, the half life of CF2 analog was found to be 45 times greater than those of phosphate. Evidentally, this difluoromethylene group greatly enhances the stability of this compound toward enzymatic dephosphorylation of the terminal phosphate group. 32

Phosphate isosteres HIV-1 integrase inhibitors and phosphate isosterism Mechanism of retroviral integration Next case is HIV-1 integrase inhibitors and phosphate isosterism. First I’ll show you the mechanism of retroviral integration. Here, you can see the first step. In this step, HIV integrase bound to viral DNA via Mg ions and catalyzed the attack of the phosphodiester viral DNA by a H2O molecule. ①HIV integrase bound to viral DNA via Mg2+ ions and catalyzed the attack of the phosphodiester viral DNA by a H2O molecule. 33

Phosphate isosteres HIV-1 integrase inhibitors and phosphate isosterism Mechanism of retroviral integration Next step, after translocating to the cell nucleus, the integrase protein promoted the attack of the host DNA. ②After translocating to the cell nucleus, the integrase protein promoted the attack of the host DNA. 34

Phosphate isosteres HIV-1 integrase inhibitors and phosphate isosterism Mechanism of retroviral integration Then, Resulting in strand transfer and cleavage of the host DNA. ③Result in strand transfer and cleavage of the host DNA. 35

Phosphate isosteres HIV-1 integrase inhibitors and phosphate isosterism Character of HIV-1 integrase inhibitors Next, the character of HIV-1 integrase inhibitors is shown in the center box. Integrase inhibitors(Diketo acid) bind to the active site Mg2+ ions in conjunction with viral DNA and acting as mimics of the transition state intermediate. Integrase inhibitors (Diketo acid) bind to the active site Mg2+ ions in conjunction with viral DNA and acting as mimics of the transition state intermediate. 36

Phosphate isosteres PNAS. 2012, 109, 7, 2251 (Merck) HIV-1 integrase inhibitors and phosphate isosterism Character of HIV-1 integrase inhibitors Merck group optimized this diketo acid lead compound (L-731988), this pyrimidinedione analog, Raltegravir was developed and licensed in US in 2007. The pyrimidinedione moiety acts as the diketo acid. 37

Summary The design and application of isosteres have inspired medicinal chemists for almost 80 years, fostering creativity toward solving a range of problems in drug design, including understanding and optimizing drugs – target interactions and specificity, improving drug permeability, reducing or redirecting metabolism, and avoiding toxicity. As an established and powerful concept in medicinal chemistry, the application of bioisosteres will continue to play an important role in drug discovery. Isosterism can also contribute to the productive application in the design and optimization of catalysts on organic chemistry. The design and application of isosteres have inspired medicinal chemists for almost 80 years, fostering creativity toward solving a range of problems in drug design, including understanding and optimizing drugs – target interactions and specificity, improving drug permeability, reducing or redirecting metabolism, and avoiding toxicity. As an established and powerful concept in medicinal chemistry, the application of bioisosteres will continue to play an important role in drug discovery. Isosterism can also contribute to the productive application in the design and optimization of catalysts on organic chemistry. 38

Presentation Name | CONFIDENTIAL 39