Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

Abstract

26The cysteine protease cruzipain is considered to be a validated target for therapeutic 27 intervention in the treatment of Chagas disease. A series of 26 new compounds 28 waswere designed, synthesized, and tested against the recombinant cruzain (Cz) to 29 map its S1/S1´ subsites. The same series was evaluated on a panel of four human 30 cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which 31 is a potential target for the treatment of cutaneous leishmaniasis. The synthesized 32 compounds are dipeptidyl nitriles designed based on the most promising 33 combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building 34 blocks). Eight compounds exhibited a K i smaller than 20.0 nM for Cz, whereas three 35 compounds met these criteria for LmCPB. The three inhibitors had an EC 50 value of 36 ca. 4 μM, thus being equipotent to benznidazole according to the anti-trypanosomal 37 effects. Our mapping approach and the respective structure-activity relationships 38 provide insights into the specific ligand-target interactions for therapeutically relevant 39 cysteine proteases. 40 41 Author Summary 42 43 Despite many achievements in identifying novel agents for the treatment of tropical 44 and neglected diseases, further research continues to be of fundamental importance.45 Our research groups have been using the cruzipain cysteine protease in its 46 recombinant form, cruzain (Cz), to identify new trypanocidal agents. Considering the 47 50 different disease states. Thus, the inhibitors were also tested against cathepsins B, 51 L, K, and S. Our results demonstrate that inhibition of these cysteine proteases can 52 be achieved by appropriate structural modifications of dipeptidyl nitriles. It was also 53 possible to identify trypanocidal agents, equipotent to benznidazole, the current drug 54 of choice used for the treatment of Chagas disease. 55 56 57 Chagas disease, aka American trypanosomiasis, is a serious health and social 58 problem in Latin America and new non-endemic areas such as Japan, East Europe, 59 and the USA. Chagas disease has an annual incidence of 30,000 new cases and 60 14,000 deaths per year. In addition, more than 70,000 million people living in areas 61 where they are at risk of contracting the disease [1]. 62 The etiological agent, the protozoa parasite Trypanosoma cruzi (T. cruzi), is 63 transmitted by blood-sucking reduviid bugs of the subfamily Triatominae [2]. The only 64 two existing drugs in the market, benznidazole and nifurtimox, show strong side 65 effects and inefficiency in the chronic stage of the disease [3,4]. New safe and 66 efficacious drugs are therefore required to address with these still unmet medical 67 needs. Initiatives such as the one launched by the Drugs for Neglected Diseases 68 (DNDi) have led to worldwide collaborative efforts to discover new therapeutic 69 targets [5]. Cruzain (Cz), a recombinant form of the enzyme cruzipain (EC 3.4.22.51) 70 [6], is the most abundant cysteine protease (CP) present in the parasite and 7...

Análise quimiométrica de seletividade nos sítios ativos de cisteíno proteases da família da papaína para o estudo de substâncias antiparasitárias e antineoplásicas

“…As dipeptidil nitrilas sintetizadas no grupo NEQUIMED, vem apresentando atividade inibitória para a cruzaína, além de terem apresentados resultados promissores em ensaios celulares associados 52,101,102,103,104 .…”

“…No grupo 4 a CatB possui uma glicina, de menor volume do grupo. A substituição em P1 de um grupo ciclopropil por um grupo isopropil-metil-benzeno em SAR explorando interações S1'-P1 em miméticos de dipeptidil nitrilas apresentou um acréscimo de 0,4 e 0,6 unidades em escala logarítmica em seu pK i , em dois protótipos com combinações de P2 e P3 diferentes, enquanto a substituição em outras proteínas não apresentou um aumento na potência 104 É necessário um inibidor que se estenda em P1 para alcançar esse resíduo. O mimético de dipeptidil nitrila cocristalizado com a CatB de código 6AY2 possui um P1 com esqueleto da cadeia lateral de arginina, porém ao invés de um grupo guanidina há um grupo ureia, considerado estrutura privilegiada em química medicinal por ser biossintetizado e eliminado no organismo humano.…”

“…A substituição em P2 de leucina por meta-clorofenilalanina em SAR explorando interações, entre quais, S2-P2, em miméticos de dipeptidil nitrilas apresentou um acréscimo de 0,9 e 1,0 unidades em escala logarítmica de pK i na CatB e CatL respectivamente, enquanto que foi deletério em outras proteínas 104 . Não é possível racionalizar a seletividade encontrada através da análise das estruturas.…”