Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments

Bhakat, Soumendranath

doi:10.1039/d0ra10359d

Cited by 12 publications

(14 citation statements)

References 112 publications

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“…Given the unusual nature of this enzyme’s structure, this also provides atomistic insights into the contribution of the nepenthesin insert and its role in side-chain heterogeneity that modulates conformational dynamics of PM V, which we hope will support further investigation into this motif and A1B subfamily proteases more broadly. Future studies will also highlight role of side-chain heterogeneity in flap opening and designing novel “open flap” inhibitors targeting PM V ( 33 , 34 ).…”

Section: Discussionmentioning

confidence: 99%

The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function

Polino¹,

Miller²,

Bhakat³

et al. 2022

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function

Polino¹,

Miller²,

Bhakat³

et al. 2022

Journal of Biological Chemistry

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“…Given the unusual nature of this enzyme’s structure, this also provides atomistic insights into the contribution of the nepenthesin insert and its role in side-chain heterogeneity that modulates conformational dynamics of PM V, which we hope will support further investigation into this motif and A1B subfamily proteases more broadly. Future studies will also highlight role of side-chain heterogeneity in flap opening and designing novel ‘open flap’ inhibitors targeting PM V (35, 36).…”

Section: Discussionmentioning

confidence: 99%

A nepenthesin insert allosterically controls catalysis in the malaria parasite protease plasmepsin V

Polino

Miller

Bhakat

et al. 2022

Preprint

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Plasmepsin V (PM V) is a pepsin-like aspartic protease essential for growth of the malaria parasite Plasmodium falciparum. Previous work has shown PM V to be an ER-resident protease that processes parasite proteins destined for export into the host cell. Depletion or inhibition of the enzyme is lethal during asexual replication within red blood cells, as well as during the formation of sexual stage gametocytes. The structure of the P. vivax PM V has been characterized by x-ray crystallography, revealing a canonical pepsin fold punctuated by structural features uncommon to secretory aspartic proteases. Here we use parasite genetics to probe these structural features by attempting to rescue lethal PM V depletion with various mutant enzymes. We find an unusual nepenthesin 1-type insert to be essential for parasite growth and PM V activity. Mutagenesis of the nepenthesin insert suggests that both its amino acid sequence and one of the two disulfide bonds that undergird its structure are required for the nepenthesin insert′s role in PM V function. Molecular dynamics simulations paired with Markov state modelling suggest that the nepenthesin insert allosterically controls PM V catalysis through multiple mechanisms.

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“…Flap loop is a single long β-hairpin structure that lies perpendicularly over the aspartic dyad (see Figure 1.A), and is believed to be involved in the substrate recognition [17][18][19][20] . There have been numerous, mostly computational, studies focused on the characterisation of aspartic protease flap loop dynamics [18,19,[21][22][23][24][25][26][27][28][29][30][31][32] . It is commonly acknowledged [25] , that the flap-loop of aspartic proteases occupies a semi-open conformation in apo state.…”

Section: Introductionmentioning

confidence: 99%

Exploring aspartic protease inhibitor binding to design selective antimalarials

Bobrovs

Basens

Drunka

et al. 2022

Preprint

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Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here we explore the selectivity determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors, and describe the critical transition states in atomistic resolution. The simulation results are compared to experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such behaviour is not observed for several other aspartic proteases. The ability to estimate compound selectivity before they are synthesized is of great importance in drug design, therefore, we expect that our approach will be useful in selective inhibitor design not only against aspartic proteases, but other enzyme classes as well.

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Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments

Abstract: Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin.

Cited by 12 publications

References 112 publications

The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function

The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function

A nepenthesin insert allosterically controls catalysis in the malaria parasite protease plasmepsin V

Exploring aspartic protease inhibitor binding to design selective antimalarials

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