New paradigm of an old target: An update on structural biology and current progress in drug design towards plasmepsin II

Dan, Nirnoy; Bhakat, Soumendranath

doi:10.1016/j.ejmech.2015.03.049

Cited by 23 publications

(12 citation statements)

References 80 publications

(77 reference statements)

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“…falciparum and tightly bind multiple FV plasmepsins of human malaria parasites, they are not selective plasmepsin inhibitors [ 40 , 63 , 79 , 80 ]. For the past 25 years, various types of peptidomimetic, non-peptidic and bi-functional compounds have been screened for possible inhibitors targeting FV plasmepsins based on criteria such as inhibition potency to plasmepsins, binding selectivity to plasmepsins over their human proteinase homologs, growth inhibition of cultured malaria parasites and cytotoxicity to mammalian cell culture [ 80 – 82 ]. Aside from this study, there were other investigations in which the inhibition of compounds was analyzed on multiple FV plasmepsins.…”

Section: Discussionmentioning

confidence: 99%

Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei

et al. 2015

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The rodent malaria parasite Plasmodium berghei is a practical model organism for experimental studies of human malaria. Plasmepsins are a class of aspartic proteinase isoforms that exert multiple pathological effects in malaria parasites. Plasmepsins residing in the food vacuole (FV) of the parasite hydrolyze hemoglobin in red blood cells. In this study, we cloned PbPM4, the FV plasmepsin gene of P. berghei that encoded an N-terminally truncated pro-segment and the mature enzyme from genomic DNA. We over-expressed this PbPM4 zymogen as inclusion bodies (IB) in Escherichia coli, and purified the protein following in vitro IB refolding. Auto-maturation of the PbPM4 zymogen to mature enzyme was carried out at pH 4.5, 5.0, and 5.5. Interestingly, we found that the PbPM4 zymogen exhibited catalytic activity regardless of the presence of the pro-segment. We determined the optimal catalytic conditions for PbPM4 and studied enzyme kinetics on substrates and inhibitors of aspartic proteinases. Using combinatorial chemistry-based peptide libraries, we studied the active site preferences of PbPM4 at subsites S1, S2, S3, S1’, S2’ and S3’. Based on these results, we designed and synthesized a selective peptidomimetic compound and tested its inhibition of PbPM4, seven FV plasmepsins from human malaria parasites, and human cathepsin D (hcatD). We showed that this compound exhibited a >10-fold selectivity to PbPM4 and human malaria parasite plasmepsin 4 orthologs versus hcatD. Data from this study furthesr our understanding of enzymatic characteristics of the plasmepsin family and provides leads for anti-malarial drug design.

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Section: Discussionmentioning

confidence: 99%

Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei

et al. 2015

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“…Later, crystal structures of uncomplexed Plm II and complexed Plm II with potent inhibitors were solved up to high resolution limits of 1.9 and 2.7 Å (Asojo et al, 2003). Mature Plm II consists of a single chain of 329 amino acids, folded in to two topologically similar N and C terminal domains (Asojo et al, 2003; Dan and Bhakat, 2015). Each domain contributes one aspartic acid residue to the catalytic dyad (Asp34 and Asp214) defining the active site (Figure 4A).…”

Section: Malaria Parasite Plasmepsins: Distinct From Other Aspartyl Pmentioning

confidence: 99%

“…Generally, transition-state analogs of the tetrahedral intermediate which bind more tightly as compared to the substrate but are resistant to enzymatic cleavage are popular as aspartic protease inhibitors. Thus, several peptidomimetics acting as transition-state isostere, based on reduced amide, statin, hydroxyethylamine scaffolds, and also small molecule inhibitors of Plm II have emerged as potential antimalarial agents (Boss et al, 2003; Ersmark et al, 2006; Dan and Bhakat, 2015). However, the major bottleneck has been the specific selectivity to pathogenic Plms and moreover selectivity toward a particular subtype of Plm.…”

Section: Malaria Parasite Plasmepsins: Distinct From Other Aspartyl Pmentioning

confidence: 99%

Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets

Mishra

Singh

2019

Front. Microbiol.

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Malaria, caused by protozoan of genus Plasmodium, remains one of the highest mortality infectious diseases. Malaria parasites have a complex life cycle, easily adapt to their host’s immune system and have evolved with an arsenal of unique proteases which play crucial roles in proliferation and survival within the host cells. Owing to the existing knowledge of enzymatic mechanisms, 3D structures and active sites of proteases, they have been proven to be opportune for target based drug development. Here, we discuss in depth the crucial roles of essential proteases in Plasmodium life cycle and particularly focus on highlighting the atypical “structural signatures” of key parasite proteases which have been exploited for drug development. These features, on one hand aid parasites pathogenicity while on the other hand could be effective in designing targeted and very specific inhibitors for counteracting them. We conclude that Plasmodium proteases are suitable as multistage targets for designing novel drugs with new modes of action to combat malaria.

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“…Due to the neglected status of Malaria, the conformational flexibility and structural biology of Plm has not generated much attention among structural and computational biologists when compared with HIV protease. 2,3,9,10 Inspired by the idea that the flap of HIV-protease spontaneously opens and close in MD simulation, 3 Karubiu et al . 11 used MD simulations and devised some distance parameters to understand the flap opening in Plm II.…”

Section: Introductionmentioning

confidence: 99%

Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

Bhakat

Söderhjelm

2020

Preprint

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Flexibility of β hairpin structure known as flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequence similarity. Tyrosine is a conserved residue present in the flap region of pepsin-like aspartic proteases. In apo protease, tyrosine remains in a dynamic equilibrium between normal and flipped states due to rotation of χ1 angle (distributions of the χ1 angle centred around radian or radian are denoted as normal, whereas distribution centred around ±π radian is denoted as flipped). In this study, we have used apo Plm-II and BACE-1 as model systems. Independent MD simulations starting with Plm-II and BACE-1 remained stuck either in normal or flipped state. Metadynamics simulations using torsion angles (χ1 and χ2 of Tyr) as CVs sampled transition between normal and flipped states. Qualitatively, flipped and normal states predicted to be equally populated. These states were stabilised by H-bond interactions to tryptophan (normal) and catalytic aspartate (flipped) respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine; reduced flap flexibility and resulted in a flap collapse. This is in accordance with previous experimental studies which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Using apo plasmepsin-II and BACE-1 as model systems, we have hypothesised that the rotation of tyrosine side-chain is the key movement which governs the flap dynamics in all pepsin-like aspartic proteases.

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New paradigm of an old target: An update on structural biology and current progress in drug design towards plasmepsin II

Cited by 23 publications

References 80 publications

Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei

Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei

Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets

Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

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