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Cyclophilin Succumbs to a Macrocyclic Chameleon Bradley C. Doak† and Jan Kihlberg*,‡ †
Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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‡
ABSTRACT: Targets that have large and groove-shaped binding sites, such as cyclophilin, are difficult to drug with small molecules. Macrocycles of natural product origin can be ideal starting points for such targets as illustrated by the transformation of sanglifehrin A into an orally bioavailable potential candidate drug. Optimization benefits from development of convergent, modular synthetic routes in combination with structure and property based methods for lead optimization.
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plasma protein binding, the second relied on introduction of an intramolecular hydrogen bond to improve cell permeability and oral absorption, and the final step reduced log D, thereby reducing metabolism and PXR related drug−drug interactions. Natural products have continued to supply a steady source of novel, therapeutically relevant leads for drug discovery,5,8 even in the eras of high-throughput screening, fragment-based lead generation, and biologics. This is beautifully illustrated by the transformation of sanglifehrin A via compound 2 into 3 and in bRo5 space by the approval of carfilzomib,5 which targets the proteasome and is used for treatment of multiple myeloma. The increasing need to conquer difficult targets using large and complex ligands has also spurred major interest in new modalities and technologies for finding leads,9 such as cyclic peptides10 and DNA encoded libraries.11 Natural products often have excellent affinity and selectivity for the target but lack cell permeability and oral absorption. Mackman et al. expertly applied rational structure and property based design to modify their macrocyclic natural product lead into a smaller, more permeable and orally bioavailable clinical candidate.20 Theirs is yet another encouraging example where rational property based optimization has been applied to larger compounds in bRo5 space contributing to the increasing mastery of this technique.12 Recent approvals of inhibitors of the hepatitis C virus NS3/4A protease and of the Bcl-2 inhibitor venetoclax used for treatment of leukemia5 further highlight our increasing ability to discover orally absorbed drugs for intracellular difficult-to-drug targets. Transformation of compound 35 into 34 stands out among the modifications employed in development of 2 into the orally bioavailable 3 (Figure 2A). It allowed for formation of a dynamic intramolecular hydrogen bond between the quinoline nitrogen and the lactam NH, and provided impressive, simultaneous improvements in cell permeability and solubility. Such environment dependent behavior led to chameleonic characteristics which can be pivotal in obtaining the required properties for oral bioavailability when working in bRo5 drug space. Molecular chameleons have only recently been researched in somewhat greater detail,13 with multiple cases being found or designed in small molecules,14,15 in drugs in
t has been proposed that half of all targets assumed to be involved in human disease cannot be modulated with small molecule drugs that comply with the rule of 5.1 Such difficultto-drug targets often have large, flat, or groove-shaped binding sites and are out of reach for biologics when found intracellularly. Compounds in “beyond rule of 5” (bRo5) space, and in particular macrocycles, have been found to be especially useful in drugging targets that have such difficult binding sites.2,3 In addition, bRo5 compounds may be cell permeable and orally available provided that properties are kept within a set of outer boundaries, e.g., MW < 1000 Da.4,5 The discovery of the HCV NS3/4A protease inhibitors and the anticancer agent venetoclax that bind to flat and groove-shaped binding sites, respectively, constitutes recent examples of successful drug discovery programs in this novel and uncharted chemical space. In this issue of the Journal of Medicinal Chemistry, Richard Mackman et al. report the optimization of a macrocyclic lead derived from the natural product sanglifehrin A into a potent and orally bioavailable inhibitor of cyclophilin as a potential anti-HCV agent.20 This work illustrates that natural products still constitute a rich source for discovery of nontraditional drugs, in particular when their synthesis can be achieved using a modular “build−couple−pair” approach.6 The cyclophilins are a family of peptidyl-prolyl isomerases that are involved in a number of biological responses. These range from immunosuppression when cyclophilin is bound to cyclosporin A to asthma and viral replication. The binding site of cyclophilin is a large, shallow, and relatively flat groove for which it has been difficult to discover potent small molecule inhibitors by screening and subsequent property based optimization. Instead, complex natural products such as cyclosporin A and the sanglifehrins constitute the most potent inhibitors for the cyclophilins. In an earlier publication the authors described how structural simplification of sanglifehrin A provided macrocycle 2 as an inhibitor of cyclophilin A, with modest anti-HCV activity but poor pharmacokinetics (Figure 1).7 In the current article Mackman et al. now report how structure guided optimization of 2 in combination with careful tuning of compound properties led to 3 as a potent inhibitor of cyclophilin A (Kd < 10 nM) and HCV-2a (EC50 < 100 nM) with high oral bioavailability in rat and dog (>55%).20 Optimization was performed in three steps where the first set of structural modifications improved potency and lowered © XXXX American Chemical Society
Received: October 5, 2018
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DOI: 10.1021/acs.jmedchem.8b01555 J. Med. Chem. XXXX, XXX, XXX−XXX
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Figure 1. Trajectory of development of sanglifehrin A into drug-like analogues 2 and 3 that inhibit cyclophilin A through the use of structure- and property-based optimization. Calculated physicochemical properties and experimentally determined in vitro properties are given adjacent to the structures of the three compounds. In vitro properties are inhibition of binding of a FRET probe to cyclophilin A (KD), permeability across Caco-2 cell monolayers in the A → B direction (Papp) and % free in human plasma (% free). The 3D cube shows the starting point sanglifehrin A, key compounds 2 and 3, as well as oral drugs having MW > 500 Da (gray dots) in TPSA, cLogP, and MW space.
Figure 2. (A) Design of compound 34 from 35 allowed formation of a dynamic intramolecular hydrogen bond which can impart chameleonic character to 34. Compound 35 has a calculated 3D polar surface area (PSA) of 132 Å2, whereas chameleon 34 can populate conformations for which the 3D PSA varies between 133 and 92 Å2 because of the dynamic intramolecular hydrogen bond (center and bottom structures, respectively). Conformers and 3D PSA were calculated by the viewpoint authors for illustrative purposes. 3D PSA was calculated based on the solvent accessible surface area of N, O, and attached H atoms, shown as red (polar), while white denotes nonpolar surfaces in the structures. Cell permeability was determined across Caco-2 cell monolayers and reported by Mackman et al.20 (B) Overview of the convergent synthetic route developed for preparation of candidate drug 3 and analogues. Compound numbers are those used by Mackman et al.
bRo5 space,16 and also in cyclic peptide systems.17 We expect
As molecular weight increases outside traditional drug-like space, compounds are likely to become more complex and their syntheses more challenging. This is a particular issue for macrocycles as the macrocyclization step is often sensitive to small structural variations and subject to low yields.18 The
that such strategies will expand the tool box used in drug design and lead to refined property guidelines that instill the “principles rather than rules”12 of property based design. B
DOI: 10.1021/acs.jmedchem.8b01555 J. Med. Chem. XXXX, XXX, XXX−XXX
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(3) Doak, B. C.; Zheng, J.; Dobritzsch, D.; Kihlberg, J. How beyond rule of 5 drugs and clinical candidates bind to their targets. J. Med. Chem. 2016, 59, 2312−2327. (4) Doak, B. C.; Over, B.; Giordanetto, F.; Kihlberg, J. Oral druggable space beyond the rule of 5: Insights from drugs and clinical candidates. Chem. Biol. 2014, 21, 1115−1142. (5) Poongavanam, V.; Doak, B. C.; Kihlberg, J. Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space. Curr. Opin. Chem. Biol. 2018, 44, 23−29. (6) Nielsen, T. E.; Schreiber, S. L. Towards the optimal screening collection: A synthesis strategy. Angew. Chem., Int. Ed. 2008, 47, 48− 56. (7) Steadman, V. A.; Pettit, S. B.; Poullennec, K. G.; Lazarides, L.; Keats, A. J.; Dean, D. K.; Stanway, S. J.; Austin, C. A.; Sanvoisin, J. A.; Watt, G. M.; Fliri, H. G.; Liclican, A. C.; Jin, D.; Wong, M. H.; Leavitt, S. A.; Lee, Y.-J.; Tian, Y.; Frey, C. R.; Appleby, T. C.; Schmitz, U.; Jansa, P.; Mackman, R. L.; Schultz, B. E. Discovery of potent cyclophilin inhibitors based on the structural simplification of sanglifehrin A. J. Med. Chem. 2017, 60, 1000−1017. (8) Newman, D. J.; Cragg, G. M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod. 2016, 79, 629−661. (9) Valeur, E.; Guéret, S. M.; Adihou, H.; Gopalakrishnan, R.; Lemurell, M.; Waldmann, H.; Grossmann, T. N.; Plowright, A. T. New modalities for challenging targets in drug discovery. Angew. Chem., Int. Ed. 2017, 56, 10294−10323. (10) Li, Y.; De Luca, R.; Cazzamalli, S.; Pretto, F.; Bajic, D.; Scheuermann, J.; Neri, D. Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold. Nat. Chem. 2018, 10, 441−448. (11) Usanov, D. L.; Chan, A. I.; Maianti, J. P.; Liu, D. R. Secondgeneration DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nat. Chem. 2018, 10, 704−714. (12) Young, R. J.; Leeson, P. D. Mapping the efficiency and physicochemical trajectories of successful optimizations. J. Med. Chem. 2018, 61, 6421−6467. (13) Whitty, A.; Zhong, M.; Viarengo, L.; Beglov, D.; Hall, D. R.; Vajda, S. Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discovery Today 2016, 21, 712−717. (14) Over, B.; Matsson, P.; Tyrchan, C.; Artursson, P.; Doak, B. C.; Foley, M. A.; Hilgendorf, C.; Johnston, S. E.; Lee, M. D.; Lewis, R. J.; McCarren, P.; Muncipinto, G.; Norinder, U.; Perry, M. W.; Duvall, J. R.; Kihlberg, J. Structural and conformational determinants of macrocycle cell permeability. Nat. Chem. Biol. 2016, 12, 1065−1074. (15) Tyagi, M.; Poongavanam, V.; Lindhagen, M.; Pettersen, A.; Sjö, P.; Schiesser, S.; Kihlberg, J. Toward the design of molecular chameleons: flexible shielding of an amide bond enhances macrocycle cell permeability. Org. Lett. 2018, 20, 5737−5742. (16) Rossi Sebastiano, M.; Doak, B. C.; Backlund, M.; Poongavanam, V.; Over, B.; Ermondi, G.; Caron, G.; Matsson, P.; Kihlberg, J. Impact of dynamically exposed polarity on permeability and solubility of chameleonic drugs beyond the rule of 5. J. Med. Chem. 2018, 61, 4189−4202. (17) Rezai, T.; Bock, J. E.; Zhou, M. V.; Kalyanaraman, C.; Lokey, R. S.; Jacobson, M. P. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J. Am. Chem. Soc. 2006, 128, 14073−14080. (18) Marsault, E.; Peterson, M. L. Macrocycles are great cycles: Applications, opportunities, and challenges of synthetic macocycles in drug discovery. J. Med. Chem. 2011, 54, 1961−2004. (19) Rosenquist, Å.; Samuelsson, B.; Johansson, P.-O.; Cummings, M. D.; Lenz, O.; Raboisson, P.; Simmen, K.; Vendeville, S.; de Kock, H.; Nilsson, M.; Horvath, A.; Kalmeijer, R.; de la Rosa, G.; BeumontMauviel, M. Discovery and development of simeprevir (TMC435), a HCV NS3/4A protease inhibitor. J. Med. Chem. 2014, 57, 1673− 1693. (20) Mackman, R. L.; Steadman, V. A.; Dean, D. K.; Jansa, P.; Poullennec, K. G.; Appleby, T.; Austin, C.; Blakemore, C. A.; Cai, R.;
HCV NS3/4A protease inhibitor simeprevir constitutes an illustrative example that used synthetic routes which often provided 4% overall yield was developed, while also reducing the number of steps significantly.19 In conclusion, a large proportion of all targets assumed to be involved in human disease have large, flat, or groove-shaped binding sites that are difficult to modulated with rule of 5 compliant drugs. When found within cells such targets are out of reach for biologics, but compounds in bRo5 space such as macrocycles of natural product origin often constitute useful starting points for oral drug discovery campaigns. As illustrated by Mackman et al.,20 development of natural products into orally administered candidate drugs benefits substantially through rigorous employment of structure and property based optimization.12 In addition, use of novel approaches, such as introduction of appropriately positioned functional groups and suitable molecular flexibility, can provide chameleonic properties.13,16 This may augment traditional strategies for optimization and provide compounds in which high solubility and cell permeability are combined with potent target binding in a more effective manner. Last but not least, development of modular, convergent synthetic routes that allow efficient preparation of analogues during lead optimization is often crucial for success. Projects with difficult to drug targets can be frustrating to progress; however recent years have provided a number of examples where perseverance and the use of rational lead optimization strategies have prevailed. We are hopeful that this evolution will continue to make drug discovery more efficient and expand oral druggable space.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Phone: +46 (0)18 4713801. ORCID
Jan Kihlberg: 0000-0002-4205-6040
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REFERENCES
(1) Surade, S.; Blundell, T. L. Structural biology and drug discovery of difficult targets: The limits of ligandability. Chem. Biol. 2012, 19, 42−50. (2) Villar, E. A.; Beglov, D.; Chennamadhavuni, S.; Porco, J. A.; Kozakov, D.; Vajda, S.; Whitty, A. How proteins bind macrocycles. Nat. Chem. Biol. 2014, 10, 723−732. C
DOI: 10.1021/acs.jmedchem.8b01555 J. Med. Chem. XXXX, XXX, XXX−XXX
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Cannizzaro, C.; Chin, G.; Chiva, J.-Y. C.; Dunbar, N. A.; Fliri, H.; Highton, A. J.; Hui, H.; Ji, M.; Jin, H.; Karki, K.; Keats, A. J.; Lazarides, L.; Lee, Y.-J.; Liclican, A.; Mish, M.; Murray, B.; Pettit, S. B.; Pyun, P.; Sangi, M.; Santos, R.; Sanvoisin, J.; Schmitz, U.; Schrier, A.; Siegel, D.; Sperandio, D.; Stepan, G.; Tian, Y.; Watt, G. M.; Yang, H.; Schultz, B. E. Discovery of a potent and orally bioavailable cyclophilin inhibitor derived from the sanglifehrin macrocycle. J. Med. Chem. 2018, DOI: 10.1021/acs.jmedchem.8b00802
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DOI: 10.1021/acs.jmedchem.8b01555 J. Med. Chem. XXXX, XXX, XXX−XXX
