Phenotypic approaches to lead discovery and optimization of antimalarial compounds

Malaria, caused by the Plasmodium parasites and vectored by mosquitos, represents a major global health problem with several hundred million cases per year and at least 400,000 deaths per year, with most of them being African children.  While much progress has been made in the last two decades and the mortality has dropped by almost 50%, there is still an urgent need for more treatments. In the past 15 years our group has worked extensively on the early development of antimalarial compounds, either from previously known antimalarial chemotypes or from repurposing existing drugs for other indications. During the course of those studies, we surveyed the original literature and ascertained that there was a very small chemical landscape being explored for malaria and that the number of well-validated targets was very small.  This survey of over 800 papers has been published as a chapter in Burger’s Medicinal Chemistry1 and a Chemical Reviews manuscript.2 

In the past 10 years my group has published a number of papers on lead optimization of antimalarial compounds with leads arising either from known antimalarial chemotypes or from targeted screens of drug libraries.  A thorough survey of literature revealed to us that antimalarial research efforts had explored a very small chemical landscape and yielded only a few well-validated targets.  This survey of over 800 papers has been published as a chapter in the new Burger’s Medicinal Chemistry1 and a Chemical Reviews manuscript.2  We concluded that existing targets and chemotypes had been exhausted, thus meaningful progress would require new discoveries in either area.  This thinking led us to develop a method for of large libraries for antimalarial activity, regardless of mechanism of action.

We executed a whole-cell phenotypic high throughput screen of over 1.2 million compounds to identify novel chemicals that kill the malaria parasite. Then, I established collaborations with 12 other groups world-wide, including basic researchers, physicians, and clinicians.  We evaluated the hits from the screen to establish mechanism of action, examine cross-activity with other protozoa, and evaluate tractability for development, which we published in Nature.3  Next, I redirected our collaborative efforts to drug development and lead optimization. The consortium was funded by the Medicines for Malaria Venture and the NIH.  Three lead series from this work (see figure) are currently in development: the dihydroisoquinolones (DHIQ’s), dihydropyridines (DHP’s), and diaminonapthoquinones (DANQ’s). 

The most advanced series from this effort is the DHIQ’s, which have recently led to a clinical candidate, SJ000557733, being approved for development by Medicines for Malaria Venture (MMV). The development and mechanism of this series were described in a PNAS paper.4,5 I assembled a collaboration between my group, the St. Jude Clinical group, the Medicines for Malaria Venture, and Eisai Pharmaceuticals in order to develop (+)-SJ000557733 and this project is now funded by the Global Health Innovative Technology Fund through completion of Phase 1. (+)-SJ000557733 has good potency in vitro with an EC50 = 23 nM and maintains similar potency against all resistant strains tested to date.  (+)-SJ000557733 is highly efficacious against P. falciparum in vivo with an ED90 = 1.7 mg/kg, significantly superior to the standard of care antimalarial drugs chloroquine and comparable to artesunate and pyronaridine.  Pharmacokinetic studies in mice, rats, and dogs have shown the compound to be well absorbed, with 60-100% oral bioavailability and reasonable clearance.  In vivo studies have demonstrated clear potential for transmission blocking through activity on the sexual stages of the parasite.  The compound is very well tolerated in vivo with no major toxicological liability based on in vitro and in vivo studies. Comparison of efficacious doses in the mouse with the results from a 7-day toxicology study in the rat predicts at least a 60-fold safety margin for (+)-SJ000557733.  We have recently shown that (+)-SJ000557733 selectively induces eryptosis in infected red cells by inhibiting a parasite protein PfATP4. Consistent with the other PfATP4 inhibitor to enter clinical development (KAE609), (+)-SJ000557733 demonstrates a fast kill rate in vivo that is identical with artesunate.  These data demonstrate (+)-SJ000557733 to be an efficacious, safe, and clinically relevant anti-malarial agent. 

The first-in-human Phase 1a study, conducted in healthy volunteers, demonstrated the safety, tolerability, and pharmacokinetic profile of SJ733.6 The subsequent Phase 1b, a human Induced Blood Stage Malaria (IBSM) challenge study in healthy volunteers, demonstrated the antimalarial pharmacodynamic effects of SJ733.6 Overall, SJ733’s excellent tolerability and safety profile, combined with its rapid antiparasitic effect, supports further development of SJ733 as an antimalarial therapy. (+)-SJ000557733 is currently in Phase 2 trial.

We have recently begun optimizing the DHP compound series. Preliminary data indicate that this series is potent, fast acting, and acts by a novel, as yet unidentified, mechanism. Current efforts are focused on understanding the drivers for bioavailability, identifying the mechanism, and studying the leads in pharmacodynamic models.  We are also beginning to work up other series discovered in the screen. 

References

  1. Guy, R. K.; Smithson, D. Antimalarials. 7th ed.; Wiley: New York, 2010; Vol. 7.
  2. Barnett, D. S.; Guy, R. K. Antimalarials in Development in 2014. Chem Rev 2014.
  3. Guiguemde, W. A.; Shelat, A. A.; Bouck, D.; Duffy, S.; Crowther, G. J.; Davis, P. H.; Smithson, D. C.; Connelly, M.; Clark, J.; Zhu, F.; Jimenez-Diaz, M. B.; Martinez, M. S.; Wilson, E. B.; Tripathi, A. K.; Gut, J.; Sharlow, E. R.; Bathurst, I.; El Mazouni, F.; Fowble, J. W.; Forquer, I.; McGinley, P. L.; Castro, S.; Angulo-Barturen, I.; Ferrer, S.; Rosenthal, P. J.; Derisi, J. L.; Sullivan, D. J.; Lazo, J. S.; Roos, D. S.; Riscoe, M. K.; Phillips, M. A.; Rathod, P. K.; Van Voorhis, W. C.; Avery, V. M.; Guy, R. K. Chemical genetics of Plasmodium falciparum. Nature 2010, 465, 311-315.
  4. Jimenez-Diaz, M. B.; Ebert, D.; Salinas, Y.; Pradhan, A.; Lehane, A. M.; Myrand-Lapierre, M. E.; O’Loughlin, K. G.; Shackleford, D. M.; Justino de Almeida, M.; Carrillo, A. K.; Clark, J. A.; Dennis, A. S.; Diep, J.; Deng, X.; Duffy, S.; Endsley, A. N.; Fedewa, G.; Guiguemde, W. A.; Gomez, M. G.; Holbrook, G.; Horst, J.; Kim, C. C.; Liu, J.; Lee, M. C.; Matheny, A.; Martinez, M. S.; Miller, G.; Rodriguez-Alejandre, A.; Sanz, L.; Sigal, M.; Spillman, N. J.; Stein, P. D.; Wang, Z.; Zhu, F.; Waterson, D.; Knapp, S.; Shelat, A.; Avery, V. M.; Fidock, D. A.; Gamo, F. J.; Charman, S. A.; Mirsalis, J. C.; Ma, H.; Ferrer, S.; Kirk, K.; Angulo-Barturen, I.; Kyle, D. E.; DeRisi, J. L.; Floyd, D. M.; Guy, R. K. (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, E5455-5462.
  5. Floyd DM, Stein P, Wang Z, Liu J, Castro S, Clark JA, Connelly M, Zhu F,Holbrook G, Matheny A, Sigal MS, Min J, Dhinakaran R, Krishnan S, Bashyum S, Knapp S, Guy RK. Hit-to-Lead Studies for the Antimalarial Tetrahydroisoquinolone Carboxanilides. J Med Chem. 2016 Sep 8;59(17):7950-62. doi:10.1021/acs.jmedchem.6b00752. Epub 2016 Aug 25. PubMed PMID: 27505686; PubMed Central PMCID: PMC5573263.
  6. Safety, tolerability, pharmacokinetics, and antimalarial efficacy of a novel Plasmodium falciparum ATP4 inhibitor SJ733: a first-in-human and induced blood-stage malaria phase 1a/b trial. Gaur AH, McCarthy JS, Panetta JC, Dallas RH, Woodford J, Tang L, Smith AM, Stewart TB, Branum KC, Freeman BB 3rd, Patel ND, John E, Chalon S, Ost S, Heine RN, Richardson JL, Christensen R, Flynn PM, Van Gessel Y, Mitasev B, Möhrle JJ, Gusovsky F, Bebrevska L, Guy RK. Lancet Infect Dis. 2020 Apr 7:S1473-3099(19)30611-5. doi: 10.1016/S1473-3099(19)30611-5. Online ahead of print. PMID: 32275867

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