Plasmodium Falciparum Enoyl Acyl Carrier Protein Reductase Research Articles

Analysis Docking Of Plasmodium Falciparum Enoyl Acyl Carrier Protein Reductase (Pfenr) With Organic Compunds From Virtual Screening Of Herbal Database

Malaria is one of problematic infectious diseases worldwide. The absence of an effective vaccine and the spread of drug resistant strains of Plasmodium clearly indicate the necessity for the deveploment of new chemotherapeutic agents. Recent method being developed is searching a new drug of antimalarial using in silico screening, or also known as virtual screening. One of enzyme target that important for growth of the malaria parasite is Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase (PfENR). Inhibition of this enzyme cause the fatty acid biosynthesis type II will be terminated. In this research, in silico screening was performed using AUTODOCK VINA software to find inhibitor candidates of PfENR by using ligands from the database of Medicinal Plants in Indonesia. On the AUTODOCK VINA software moleculer docking experiments were performed between ligands and macromolecule target PfENR. This target that has been optimized with residue removal and charges addition. Ligand is expected to be the PfENR inhibitors.

Molecular Docking Studies of Potential Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside as Inhibitor antimalaria

The purpose of this research is to analysis the potential Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside as an inhibitor Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase (PfENR) compound for antimalaria. The method used to analysis the potential Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside as an antimalaria was insilico approach by molecular docking using Autodock Vina. Based on the free energy parameter analized ΔG, the value of free energy ΔG is -11.6 kcal / mol with 5 repetisions. The free energy ΔG value from the analysis results was relatively low, this means that Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside is stable to be used as an inhibitor of Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase (PfENR). Because the lower the free energy of a molecule the more stable the molecule. Based on hydrogen bond parameters, there were hydrogen bonds in Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside and PfENR receptors. This shows that Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside binding PfENR receptors to strong and stable. Based on the parameters of the analysis of Ligand and Receptor Interactions also showed that Quercetin 3,4’-dimethyl ether 7-alpha-LArabinofuranosyl-(1-6)-glucoside compounds were stable used as Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase (PfENR) inhibitors for antimalaria.

Identification of PfENR inhibitors: A hybrid structure-based approach in conjunction with molecular dynamics simulations.

In the current study, we have constructed receptor-based pharmacophore models by exploiting the Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) structural proteome. The derived models were subjected to a series of validation procedures to list the representative hypotheses that can be used for the screening of the Drug-like Diverse Database. A set of 739 molecules was retrieved and analyzed for the adsorption, distribution, metabolism, excretion and toxicity (ADMET) and drug-likeness attributes. The filtered drug-like molecules (64) were then subjected to molecular docking and HYDE assessment studies. The hybrid structure-based approach yielded 4 molecules, UKR1308259, ENA1096786, UKR403454, and ASI51224, as PfENR inhibitors. The stability of these inhibitors was assessed using molecular mechanics-generalized born surface area approach-based free binding energy calculations and molecular dynamics simulations. Molecular mechanics-generalized born surface area calculations and molecular dynamics simulations showed that UKR1308259, ENA1096786, and ASI51224 were more potent PfENR inhibitors. The rationale behind the current work was to identify orally available inhibitor molecules with diverse scaffolds that could serve as initial leads for the drug design against PfENR.

IN-SILICO SCREENING AGAINST ANTIMALARIAL TARGET PLASMODIUM FALCIPARUM ENOYL-ACYL CARRIER PROTEIN REDUCTASE

Objective: Malaria is a parasitic infection that causes worldwide health problems. The absence of an effective vaccine and Plasmodium strains that are resistant to antimalarial drugs emphasize the importance of developing new chemotherapeutic agents. The use of computers for in-silico screening, or virtual screening, is currently being developed as a method for discovering antimalarial drugs. One of the enzymes that can support the development of the malaria parasite is the Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR). Inhibition of these enzymes leads to Type II lipid biosynthesis inhibition on the parasite.Methods: This research investigates the use of virtual screening to find PfENR inhibitor candidates. A molecular docking method using GOLD software and the medicinal plants in Indonesia database will be used. This target has been optimized by the removal of residues and the addition of charge. Ligand is expected to be an inhibitor of PfENR.Results: In-silico screening, or virtual screening, found that the top five compounds with the highest GOLD score at trial are kaempferol 3-rhamnosyl- (1-3)-rhamnosyl-(1-6)-glucoside; cyanidin 3,5-di-(6-malonylglucoside); 8-hydroxyapigenin 8-(2’’, 4’’-disulfato glucuronide); epigallocatechin 3,5,-di- O-gallat; quercetin 3,4’-dimethyl ether 7-alpha-L-arabinofuranosyl-(1-6)-glucoside. They had GOLD scores of 94.73, 95.90, 86.46, 85.39, and 84.40, respectively.Conclusions: There are two candidate inhibitor compounds from tea (Camellia sinensis), which have potential for development as an antimalarial drug, which are kaempferol 3-rhamnosyl-(1-3)-rhamnosyl-(1-6)-glucoside and epigallocatechin 3,5,-di-O-gallate, with a GOLD score of 94.73 and 85.39, respectively.

Natural Compounds as Inhibitors of Plasmodium Falciparum Enoyl-acyl Carrier Protein Reductase (PfENR): An In silico Study

Natural Compounds as Inhibitors of Plasmodium Falciparum Enoyl-acyl Carrier Protein Reductase (PfENR): An In silico Study

Prioritization of active antimalarials using structural interaction profile of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR)-triclosan derivatives

An empirical relationship between the experimental inhibitory activities of triclosan derivatives and its computationally predicted Plasmodium falciparum enoyl-acyl carrier protein (ACP) reductase (PfENR) dock poses was developed to model activities of known antimalarials. A statistical model was developed using 57 triclosan derivatives with significant measures (r = 0.849, q2 = 0.619, s = 0.481) and applied on structurally related and structurally diverse external datasets. A substructure-based search on ChEMBL malaria dataset (280 compounds) yielded only two molecules with significant docking energy, whereas eight active antimalarials (EC50 < 100 nM, tested on 3D7 strain) with better predicted activities (pIC50 ~ 7) from Open Access Malaria Box (400 compounds) were prioritized. Further, calculations on the structurally diverse rhodanine molecules (known PfENR inhibitors) distinguished actives (experimental IC50 = 0.035 μM; predicted pIC50 = 6.568) and inactives (experimental IC50 = 50 μM; predicted pIC50 = -4.078), which showed that antimalarials possessing dock poses similar to experimental interaction profiles can be used as leads to test experimentally on enzyme assays.

Integrating molecular docking, CoMFA analysis, and machine-learning classification with virtual screening toward identification of novel scaffolds as Plasmodium falciparum enoyl acyl carrier protein reductase inhibitor

In the present study, an integrated application of various in silico methods including molecular docking, CoMFA analyses, and machine-learning classification methods were used on a set of known triclosan and rhodanine inhibitors of Plasmodium falciparum enoyl acyl carrier protein reductase (PfENR) and Maybridge compound database with the prime objective of implementation of knowledge-based synergistic approach toward prioritized screening and identification of novel scaffolds as PfENR inhibitors. Ensemble of CoMFA models were build with excellent values of statistical matrices where genetic algorithm was applied in a conformation selection step on a dataset clustered over chemical space to ensure high degree of structural variability with correlation. Two-dimensional and three-dimensional descriptors were used vigorously to classify actives from inactives by extracting useful correlation among selected descriptors. Nevertheless, the entire hypothesis was pipelined sequentially in the pursuit of proposing probable actives from Maybridge database on the basis of docking, machine learning classification, and CoMFA studies. After ADME filtering, a set of 26 compounds from the Maybridge database were finally predicted to be plausible inhibitors of PfENR satisfying multiple computational validation models.

Molecular modeling studies, synthesis, and biological evaluation of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) inhibitors

The search for new antimalarial agents is necessary as current drugs in the market become vulnerable due to the emergence of resistance strains of Plasmodium falciparum (P. falciparum). The biosynthetic pathway for fatty acids has been recognized and validated as an important drug target in P.falciparum. One of the important enzymes in this pathway that has a determinant role in completing the cycles of chain elongation is Enoyl-ACP reductase (ENR) also popularly known as FabI. In this paper we report the design, synthesis, and microbial evaluation of inhibitors of Plasmodium enoyl reductase (PfENR). The search for inhibitors involved a virtual screening of the iResearch database with docking simulations. One of the hits was selected and modified to optimize its binding to PfENR; this resulted in the development of analogues of N-benzylidene-4-phenyl-1,3-thiazol-2-amine. The activity of these analogues was predicted from comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models constructed from a dataset of 43 known inhibitors of PfENR. The most promising molecules were synthesized and their structures characterized by spectroscopic techniques. The molecules were screened for in vitro antimalarial activity by whole-cell assay method. Two molecules, viz. VRC-007 and VRC-009, were found to be active at 4.67 and 7.01 microM concentrations, respectively.

X-ray Structural Analysis of Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase as a Pathway toward the Optimization of Triclosan Antimalarial Efficacy

The x-ray crystal structures of five triclosan analogs, in addition to that of the isoniazid-NAD adduct, are described in relation to their integral role in the design of potent inhibitors of the malarial enzyme Plasmodium falciparum enoyl acyl carrier protein reductase (PfENR). Many of the novel 5-substituted analogs exhibit low micromolar potency against in vitro cultures of drug-resistant and drug-sensitive strains of the P. falciparum parasite and inhibit purified PfENR enzyme with IC50 values of <200 nM. This study has significantly expanded the knowledge base with regard to the structure-activity relationship of triclosan while affording gains against cultured parasites and purified PfENR enzyme. In contrast to a recent report in the literature, these results demonstrate the ability to improve the in vitro potency of triclosan significantly by replacing the suboptimal 5-chloro group with larger hydrophobic moieties. The biological and x-ray crystallographic data thus demonstrate the flexibility of the active site and point to future rounds of optimization to improve compound potency against purified enzyme and intracellular Plasmodium parasites.

Discovery of a Rhodanine Class of Compounds as Inhibitors of Plasmodium falciparum Enoyl-Acyl Carrier Protein Reductase

Enoyl acyl carrier protein (ACP) reductase, one of the enzymes of the type II fatty acid biosynthesis pathway, has been established as a promising target for the development of new drugs for malaria. Here we present the discovery of a rhodanine (2-thioxothiazolidin-4-one) class of compounds as inhibitors of this enzyme using a combined approach of rational selection of compounds for screening, analogue search, docking studies, and lead optimization. The most potent inhibitor exhibits an IC(50) of 35.6 nM against Plasmodium falciparum enoyl ACP reductase (PfENR) and inhibits growth of the parasite in red blood cell cultures at an IC(50) value of 750 nM. Many more compounds of this class were found to inhibit PfENR at low nanomolar to low micromolar concentrations, expanding the scope for developing new antimalarial drugs. The structure-activity relationship of these rhodanine compounds is discussed.

Synthesis and biological activity of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 2: 2′-Substituted triclosan derivatives

2′-Substituted analogs of triclosan have been synthesized to target inhibition of the key malarial enzyme Plasmodium falciparum enoyl acyl carrier protein reductase (PfENR). Many of these compounds exhibit good potency (EC 50 < 500 nM) against in vitro cultures of drug-resistant and drug-sensitive strains of the P. falciparum parasite and modest (IC 50 = 1–20 μM) potency against purified PfENR enzyme. Compared to triclosan, this survey of 2′-substituted derivatives has afforded gains in excess of 20- and 30-fold versus the 3D7 and Dd2 strains of parasite, respectively.

Synthesis, biological activity, and X-ray crystal structural analysis of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 1: 4′-Substituted triclosan derivatives

A structure-based approach has been taken to develop 4′-substituted analogs of triclosan that target the key malarial enzyme Plasmodium falciparum enoyl acyl carrier protein reductase (PfENR). Many of these compounds exhibit nanomolar potency against purified PfENR enzyme and modest (2–10 μM) potency against in vitro cultures of drug-resistant and drug-sensitive strains of the P. falciparum parasite. X-ray crystal structures of nitro 29, aniline 30, methylamide 37, and urea 46 demonstrate the presence of hydrogen-bonding interactions with residues in the active site and point to future rounds of optimization to improve compound potency against purified enzyme and intracellular parasites.