Computational perspectives into plasmepsins structure-function relationship: implications to inhibitors design

scientific article

Computational perspectives into plasmepsins structure-function relationship: implications to inhibitors design is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

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P356DOI10.1155/2011/657483
P932PMC publication ID3134243
P698PubMed publication ID21760810
P5875ResearchGate publication ID51494157

P50authorPedro A ValienteQ56599893
Alejandro Gil-LeyQ86709485
Tirso PonsQ40459651
P2093author name stringPedro G Pascutti
Alejandro Gil L
P2860cites workThat Was Then But This Is Now: Malaria Research in the Time of an Eradication AgendaQ22061808
Genome sequence of the human malaria parasite Plasmodium falciparumQ22122524
Recombinant expression and enzymatic subsite characterization of plasmepsin 4 from the four Plasmodium species infecting man.Q45002397
Critical roles for the digestive vacuole plasmepsins of Plasmodium falciparum in vacuolar functionQ45011108
Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancyQ45112972
The role of Plasmodium falciparum food vacuole plasmepsinsQ45129812
Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active siteQ45150900
Search for substrate-based inhibitors fitting the S2' space of malarial aspartic protease plasmepsin II.Q45165701
Computer-aided design and synthesis of nonpeptidic plasmepsin II and IV inhibitorsQ46408285
X-ray structure of plasmepsin II complexed with a potent achiral inhibitorQ46445865
Structural and active site analysis of plasmepsins of Plasmodium falciparum: potential anti-malarial targetsQ46767937
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitorsQ47655078
Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductasesQ47742338
Screening aspartyl proteases with combinatorial libraries.Q47829651
Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations.Q50143963
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.Q51664708
Alternative to consensus scoring--a new approach toward the qualitative combination of docking algorithms.Q51915270
Knowledge-based scoring function to predict protein-ligand interactions.Q52083236
Ligand solvation in molecular docking.Q52214239
A general and fast scoring function for protein-ligand interactions: a simplified potential approach.Q52222006
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.Q52230454
A fast flexible docking method using an incremental construction algorithm.Q52298930
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.Q52324255
AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactionsQ53341450
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.Q53678858
An innovative application of the "flexible" GRID/PCA computational method: study of differences in selectivity between PGAs from Escherichia coli and a Providentia rettgeri mutant.Q54501737
Mapping selectivity and specificity of active site of plasmepsins from Plasmodium falciparum using molecular interaction field approachQ56435972
Kinetic analysis of plasmepsins I and II aspartic proteases of the Plasmodium falciparum digestive vacuoleQ71622814
Binding free energy calculations for P450cam-substrate complexesQ71623180
A new method for predicting binding affinity in computer-aided drug designQ72408636
Ligand binding affinity prediction by linear interaction energy methodsQ74505232
Hemoglobin-degrading plasmepsin II is active as a monomerQ79240095
Additional interaction of allophenylnorstatine-containing tripeptidomimetics with malarial aspartic protease plasmepsin IIQ80075132
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring functionQ80287324
Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free EnergiesQ86855672
Potencies of human immunodeficiency virus protease inhibitors in vitro against Plasmodium falciparum and in vivo against murine malariaQ24538763
Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparumQ24597864
Plasmepsin V licenses Plasmodium proteins for export into the host erythrocyteQ24644157
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databasesQ27231136
Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370Q27640033
Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparumQ27640611
Recombinant Plasmepsin 1 from the Human Malaria Parasite Plasmodium falciparum : Enzymatic Characterization, Active Site Inhibitor Design, and Structural AnalysisQ27654043
Crystal Structures of the Histo-Aspartic Protease (HAP) from Plasmodium falciparumQ27654096
A Plasmodium falciparum dipeptidyl aminopeptidase I participates in vacuolar hemoglobin degradationQ27972584
Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3Q27973740
Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engineQ28207735
Development and validation of a genetic algorithm for flexible dockingQ28236574
Sequence, expression and modeled structure of an aspartic proteinase from the human malaria parasite Plasmodium falciparumQ28239261
Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoringQ28246329
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracyQ28251042
Virtual screening strategies in drug discoveryQ28253252
eHiTS: a new fast, exhaustive flexible ligand docking systemQ28253448
Hemoglobin degradation in the malaria parasite Plasmodium falciparum: an ordered process in a unique organelleQ28972254
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibilityQ29547658
An evolutionary trace method defines binding surfaces common to protein familiesQ29615880
Improved protein-ligand docking using GOLDQ29616787
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screeningQ29617343
Identification and characterization of falcilysin, a metallopeptidase involved in hemoglobin catabolism within the malaria parasite Plasmodium falciparumQ30042132
Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidineQ30042887
Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: a catabolic pathway initiated by a specific aspartic proteaseQ30045945
FlexE: efficient molecular docking considering protein structure variations.Q30328164
A computational procedure for determining energetically favorable binding sites on biologically important macromoleculesQ30406755
Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II.Q30672366
Sensitivity of an empirical affinity scoring function to changes in receptor-ligand complex conformationsQ30689339
Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor.Q30827566
Computational modelling of inhibitor binding to human thrombinQ30982674
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activityQ31034495
Structure and mechanism of the pepsin-like family of aspartic peptidasesQ35021899
Inhibitors of the Plasmodium falciparum parasite aspartic protease plasmepsin II as potential antimalarial agentsQ35100335
Functional expression of falcipain, a Plasmodium falciparum cysteine proteinase, supports its role as a malarial hemoglobinase.Q35415207
Free energy calculations and ligand bindingQ35590736
Computational approaches to model ligand selectivity in drug design.Q36384971
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.Q37014096
Docking, virtual high throughput screening and in silico fragment-based drug designQ37296002
Current status of malaria chemotherapy and the role of pharmacology in antimalarial drug research and developmentQ37587440
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.Q37781709
Building an infrastructure for scientific Grid computing: status and goals of the EGEE projectQ38456632
The aspartic proteinase from the rodent parasite Plasmodium berghei as a potential model for plasmepsins from the human malaria parasite, Plasmodium falciparum.Q38526967
Expression and characterisation of plasmepsin I from Plasmodium falciparumQ38530094
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Role of Plasmodium falciparum digestive vacuole plasmepsins in the specificity and antimalarial mode of action of cysteine and aspartic protease inhibitorsQ39947285
Characterization of events preceding the release of malaria parasite from the host red blood cellQ40398772
What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?Q41607783
Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparumQ41745894
Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities.Q42550712
New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexesQ42908159
Pyrrolidine derivatives as plasmepsin inhibitors: binding mode analysis assisted by molecular dynamics simulations of a highly flexible proteinQ43180983
Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations.Q43480874
Activity and inhibition of plasmepsin IV, a new aspartic proteinase from the malaria parasite, Plasmodium falciparumQ43923777
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leadsQ44114180
Plasmepsin inhibitors: design, synthesis, inhibitory studies and crystal structure analysisQ44244370
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sitesQ44247315
High-affinity inhibition of a family of Plasmodium falciparum proteases by a designed adaptive inhibitorQ44511791
General model for estimation of the inhibition of protein kinases using Monte Carlo simulationsQ44871650
Ligand binding affinities from MD simulations.Q31080599
Trends in virtual combinatorial library designQ31120448
C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictionsQ31151933
Plasmepsin 4, the food vacuole aspartic proteinase found in all Plasmodium spp. infecting man.Q33193846
Binding affinity prediction with different force fields: examination of the linear interaction energy methodQ33202843
Efficient evaluation of binding free energy using continuum electrostatics solvationQ33208396
Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide librariesQ33211575
The computer program LUDI: a new method for the de novo design of enzyme inhibitorsQ33214112
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulationsQ33223342
Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV.Q33227803
Virtual ligand screening: strategies, perspectives and limitationsQ33247681
Plasmepsins as potential targets for new antimalarial therapyQ33250030
The potential of P1 site alterations in peptidomimetic protease inhibitors as suggested by virtual screening and explored by the use of C-C-coupling reagentsQ33253061
Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparumQ33255678
Design of new plasmepsin inhibitors: a virtual high throughput screening approach on the EGEE gridQ33295426
WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructuresQ33437882
alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteasesQ33487551
Library screening by fragment-based dockingQ33498543
Identification of inhibitors for putative malaria drug targets among novel antimalarial compoundsQ33682916
New class of small nonpeptidyl compounds blocks Plasmodium falciparum development in vitro by inhibiting plasmepsinsQ33982942
Order and specificity of the Plasmodium falciparum hemoglobin degradation pathwayQ34139669
A geometric approach to macromolecule-ligand interactionsQ34280176
A method to predict functional residues in proteinsQ34310572
Molecular characterization and inhibition of a Plasmodium falciparum aspartic hemoglobinase.Q34350086
Docking and scoring in virtual screening for drug discovery: methods and applicationsQ34364227
Computer-based de novo design of drug-like moleculesQ34438895
Plasmodium falciparum, P. vivax, and P. malariae: a comparison of the active site properties of plasmepsins cloned and expressed from three different species of the malaria parasiteQ34446519
Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles.Q34503862
The linear interaction energy method for predicting ligand binding free energiesQ34506720
Plasmodium falciparum cysteine protease falcipain-1 is not essential in erythrocytic stage malaria parasitesQ34514862
Further development and validation of empirical scoring functions for structure-based binding affinity predictionQ34526566
Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets.Q34548661
Plasmodium falciparum ensures its amino acid supply with multiple acquisition pathways and redundant proteolytic enzyme systemsQ34645537
The integration of genomic and structural information in the development of high affinity plasmepsin inhibitorsQ34999498
P275copyright licenseCreative Commons Attribution 3.0 UnportedQ14947546
P6216copyright statuscopyrightedQ50423863
P304page(s)657483
P577publication date2011-07-03
P1433published inJournal of Tropical MedicineQ26842862
P1476titleComputational perspectives into plasmepsins structure-function relationship: implications to inhibitors design
P478volume2011

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cites work (P2860)
Q56374979Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights
Q40766306Flap flexibility amongst plasmepsins I, II, III, IV, and V: Sequence, structural, and molecular dynamics analyses
Q37973268Microbial and fungal protease inhibitors--current and potential applications
Q38109627Trafficked Proteins-Druggable in Plasmodium falciparum?

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