Identification of Novel Malarial Cysteine Protease Inhibitors Using Structure-Based Virtual Screening of a Focused Cysteine Protease Inhibitor Library

Abstract

Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.

New approaches in antimalarial drug discovery and development: a review

“…New drugs are designed based on previous leads and the stabilities of the ligands inside the binding pockets are further verified using molecular dynamics simulations. A large variety of new antimalarial candidates has been identified using MM among new and well-established drug targets, such as enzymes involved in the folate cycle (SHMT and DHFR-TS) (França et al 2004, da Silva et al 2010, LDH (Penna-Coutinho et al 2011), enoyl-acyl carrier protein reductase (ENR) (Nicola et al 2007), protein kinases (Keenan et al 2005), cysteine proteases (Shah et al 2011), topoisomerases (Roy et al 2011) and spermidine synthase (SpdSyn) (Jacobsson et al 2008). …”

Structure of the Enterovirus 71 3C Protease in Complex with NK-1.8k and Indications for the Development of Antienterovirus Protease Inhibitor

“…According to the mode of inhibitor-protein interaction, peptidomimetic inhibitors are subdivided into the reversible inhibitors (e.g., aldehydes, nitriles, ␣-keto amides) and the irreversible inhibitors (e.g., ␣,␤-unsaturated esters, disulfides), among which the activity of the inhibitors is proportional to the electrophilicity of the reactive group (9). Although these peptidomimetic inhibitors potently inhibit the enzymatic activity, the covalent irreversible modifiers are not considered potential drug candidates, being limited by the poor selectivity resulting from the strongly reactive electrophiles and the potential toxicity caused by the formation of protein adducts (11). Therefore, success with the development of anti-EV71 protease inhibitors (PIs) remains challenging.…”

Development of Plasmodium falciparum Protease Inhibitors in the Past Decade (2002–2012)

“…Further work is required in order to improve the selectivity of these compounds because they resulted to be slightly more active against human cathepsins than FP2. Several other non-peptidic small inhibitors of FPs have been found [118][119][120][121], some of them through computerbased drug design and virtual screening studies, for instance, compounds 36-39 (Fig. 29) [94][95][96]120].…”