In Silico Study Reveals How E64 Approaches, Binds to, and Inhibits Falcipain-2 of Plasmodium falciparum that Causes Malaria in Humans

Abstract

Plasmodium falciparum malaria, which degrades haemoglobin through falcipain-2 (FP2), is a serious disease killing 445 thousand people annually. Since the P. falciparum’s survival in humans depends on its ability to degrade human’s haemoglobin, stoppage or hindrance of FP2 has antimalarial effects. Therefore, we studied the atomic details of how E64 approaches, binds to, and inhibits FP2. We found that E64 (1) gradually approaches FP2 by first interacting with FP2’s D170 and Q171 or N81, N77, and K76; (2) binds FP2 tightly (ΔGbinding = −12.2 ± 1.1 kJ/mol); and (3) persistently blocks access to FP2’s catalytic residues regardless of whether or not E64 has already been able to form a covalent bond with FP2’s C42. Furthermore, the results suggest that S41, D234, D170, N38, N173, and L172 (which are located in or near the FP2’s catalytic site’s binding pocket) contribute the most towards the favourable binding of E64 to FP2. Their in silico mutations adversely affect E64-FP2 binding affinity with D234L/A, N173L/A, W43F/A, D234L/A, H174F/A, and N38L/A having the most significant adverse effects on E64-FP2 binding and interactions. The findings presented in this article, which has antimalarial implications, suggest that hydrogen bonding and electrostatic interactions play important roles in E64-FP2 binding, and that a potential FP2-blocking E64-based/E64-like antimalarial drug should be capable of being both hydrogen-bond donor and acceptor, and/or have the ability to favourably interact with polar amino acids (such as S41, S149, N38, N173, N77, Q171) and with charged amino acids (such as D234, D170, H174) of FP2. The abilities to favourably interact with ASN, ASP, and SER appears to be important characteristics that such potential drug should have.

Design, synthesis and biological evaluation of several aromatic substituted chalcones as antimalarial agents

“…(Figures 3 and 4). This shows that the CC2 has comparatively less binding toward 3BPF compared to E64, as it blocks more catalytic residues like N‐38, N‐81, H‐174, C‐42, Q‐171, C‐39, G‐40 and G‐82 (Salawu, 2018). The results also show the CC2 has got significant binding toward FP‐2 through Cys 42 binding.…”

“…The crystal structure is also available in Protein data bank as 3BPF. The E64 proceeds toward FP-2 and binds with it tightly and inhibit it (Salawu, 2018).…”

Targeting the nsp2 Cysteine Protease of Chikungunya Virus Using FDA Approved Library and Selected Cysteine Protease Inhibitors

“…The high docking score and strong interaction via multiple non-covalent bonds resemble with the binding energy, −31.659 kcal/mol and glide emodel energy −37.219 kcal/mol. E-64 has also shown binding with Falcipain-2 of P. falciparum via hydrogen bonding and electrostatic interactions [37]. Another cysteine protease inhibitor, Leupeptin hemisulfate, has also shown significant docking score (−7.08 kcal/mol) and binding energy (−44.461 kcal/mol) and it is interacting with Trp1084 via hydrogen bond along with Q1241 and D1246 residue.…”

Protein-Protein Interactions in Malaria: Emerging Arena for Future Chemotherapeutics

“…Several inhibitors were designed based on the interactions of the FP2 and the active site inhibitor E64. Molecular dynamics (MD) simulations indicated that two sets of residues, namely, recruiter groups A (rgA) and B (rgB) (rgA (D170, Q171, C168, G169, A151, and G230); rgB (K76, N77, and N81)) of FP2 are primarily involved in the initial binding with E64 about 80% and 14% of the time, respectively, before finally proceeding to bind with the active site residues [16]. Efforts elsewhere have focused on selective inhibition of falcipains rather than indiscriminate inhibition including its human host cathepsin isoforms.…”