Structure-Based Rational Screening of Novel Hit Compounds with Structural Diversity for Cytochrome P450 Sterol 14α-Demethylase from Penicillium digitatum

In silico and in vitro evaluation of extract derived from Dunaliella salina, a halotolerant microalga for its antifungal and antibacterial activity

In the present study little explored halotolerant wall-less green alga Dunaliella salina was found to be a potent source of antibacterial and antifungal biomolecules. Both the target pathogens, bacteria (Escherischia coli, Klebsiella pneumoniae, and Acinetobacter baumannii) and fungi (Candida albicans, C. tropicalis, and Cryptococus sp.) were WHO prioritized. The bioassay guided approach led us to evaluate antibacterial and antifungal lead molecule(s) from an array of compounds using spectroscopic and in silico studies. The methanol derived crude extract was purified via thin layer chromatography (TLC) using solvent system methanol: chloroform (1:19). Maximum antimicrobial activity was observed in fractions D5, D6 and D7, the components of which were then recognized using high resolution-liquid chromatography/mass spectroscopy (Orbitrap) (HR-LC/MS). The screened compounds were then docked with target enzymes sterol-14-alpha demethylase and OmpF porin protein. The energy scores revealed that amongst all, lariciresinol-4-O-glucoside showed better binding affinity, in silico, using the Schrödinger Maestro 2018-1 platform. The 3-dimensional crystal structures of both the proteins were retrieved from the protein data bank (PDB), and showed binding energies of -14.35 kcal/mol, and -11.0 kcal/mol against respective drug targets. The molecular dynamics (MD) simulations were performed for 100 ns, using Desmond package, Schrödinger to evaluate the conformational stability and alteration of protein-ligand complexes during the simulation. Thus, our findings confirmed that lariciresinol-4-O-glucoside, a lignan derivative and known strong antioxidant, may be used as an important "lead" molecule to be developed as antibacterial and antifungal drugs in the future.Communicated by Ramaswamy H. Sarma.

Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies

This research aims to find out whether the 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a particular protein with a ligand. We are interested in using molecular docking and molecular dynamics modeling to investigate the interaction between the derivatives of 1, 2, 4-triazine with enzyme Lanosterol 14-demethylase (CYP51) of Candida albicans. The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identify the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.

Development of specific and selective bactericide by introducing exogenous metabolite of pathogenic bacteria

The widespread and repeated use of broad-spectrum bactericides has led to an increase in resistance. Developing novel broad-spectrum bactericides cannot solve the resistance problem, and may even aggravate it. The design of specific and selective bactericides has become urgent. A specific bactericidal design strategy was proposed by introducing exogenous metabolites in this study. This strategy was used to optimize two known antibacterial agents, luteolin (M) and Isoprothiolane (D), against Xoo. Based on the prodrug principles, target compound MB and DB were synthesized by combing M or D with exogenous metabolites, respectively. Bactericidal activity test results demonstrated that while the antibacterial ability of target compounds was significantly improved, their selectivity was also well enhanced by the introducing of exogenous metabolites. Comparing with the original compound, the antibacterial activity of target compound was significantly increased 92.0% and 74.5%, respectively. The optimized target compounds were more easily absorbed, and the drug application concentrations were much lower than those of the original agents, which would greatly reduce environmental pollution and relieve resistance risk. Our proposed strategy is of great significance for exploring the specific and selective bactericides against other pathogens.

Discovery of Novel Fungal Lanosterol 14α-Demethylase (CYP51)/Histone Deacetylase Dual Inhibitors to Treat Azole-Resistant Candidiasis

Invasive fungal infections (particularly candidiasis) are emerging as severe infectious diseases worldwide. Because of serious antifungal drug resistance, therapeutic efficacy of the current treatment for candidiasis is limited and associated with high mortality. However, it is highly challenging to develop novel strategies and effective therapeutic agents to combat drug resistance. Herein, the first generation of lanosterol 14α-demethylase (CYP51)-histone deacetylase (HDAC) dual inhibitors was designed, which exhibited potent antifungal activity against azole-resistant clinical isolates. In particular, compounds 12h and 15j were highly active both in vitro and in vivo to treat azole-resistant candidiasis. Antifungal mechanism studies revealed that they acted by blocking ergosterol biosynthesis and HDAC catalytic activity in fungus, suppressing the function of efflux pump, yeast-to-hypha morphological transition, and biofilm formation. Therefore, CYP51-HDAC dual inhibitors represent a promising strategy to develop novel antifungal agents against azole-resistant candidiasis.

Pharmacophore-Based Virtual Screening of Novel Inhibitors and Docking Analysis for CYP51A from Penicillium italicum

Sterol 14α-demethylases from Cytochrome P450 family (CYP51s) are essential enzymes in sterol biosynthesis and well-known as the target of antifungal drugs. The 3D structure of CYP51A from Penicillium italicum (PiCYP51A) was constructed through homology modeling based on the crystal structure of human CYP51A (PDB: 3LD6). Molecular dynamics (MD) simulation was operated to relax the initial model and followed by quality assessment using PROCHECK program. On the basis of the docking information on the currently available CYP51s with the patent demethylase inhibitors (DMIs), pharmacophore-based virtual screening combined with docking analysis was performed to pick out twelve new compounds from ZINC database. Six hits revealed in the ligand database suggested potential ability to inhibit PiCYP51A. Compared to patent fungicide triazolone, the top three lead compounds had similar or higher affinity with the target enzyme, and accordingly, exhibited comparable or lower EC50 values to P. italicum isolates. The results could provide references for de novo antifungal drug design.

Synthesis, Molecular Docking Studies, and Antifungal Activity Evaluation of New Benzimidazole-Triazoles as Potential Lanosterol 14α-Demethylase Inhibitors

Due to anticandidal importance of azole compounds, a new series of benzimidazole-triazole derivatives(5a–5s)were designed and synthesized as ergosterol inhibitors. The chemical structures of the target compounds were characterized by spectroscopic methods. The final compounds were screened for antifungal activity againstCandida glabrata(ATCC 90030),Candida krusei(ATCC 6258),Candida parapsilosis(ATCC 22019), andCandida albicans(ATCC 24433). Compounds5iand5sexhibited significant inhibitory activity againstCandidastrains with MIC50values ranging from 0.78 to 1.56 μg/mL. Cytotoxicity results revealed that IC50values of compounds5iand5sagainst NIH/3T3 are significantly higher than their MIC50values. Effect of the compounds5iand5sagainst ergosterol biosynthesis was determined by LC-MS-MS analysis. Both compounds caused a significant decrease in the ergosterol level. The molecular docking studies were performed to investigate the interaction modes between the compounds and active site of lanosterol 14-α-demethylase (CYP51), which is as a target enzyme for anticandidal azoles. Theoretical ADME predictions were also calculated for final compounds.

Targeting CYP51 for drug design by the contributions of molecular modeling

CYP51 is an enzyme of sterol biosynthesis pathway present in animals, plants, protozoa and fungi. This enzyme is described as an important drug target that is still of interest. Therefore, in this work, we reviewed the structure and function of CYP51 and explored the molecular modeling approaches for the development of new antifungal and antiprotozoans that target this enzyme. Crystallographic structures of CYP51 of some organisms have already been described in the literature, which enable the construction of homology models of other organisms' enzymes and molecular docking studies of new ligands. The binding mode and interactions of some new series of azoles with antifungal or antiprotozoan activities has been studied and showed important residues of the active site. Molecular modeling is an important tool to be explored for the discovery and optimization of CYP51 inhibitors with better activities, pharmacokinetics, and toxicological profiles.

Azole fungicides - understanding resistance mechanisms in agricultural fungal pathogens

Plant fungal pathogens can have devastating effects on a wide range of crops, including cereals and fruit (such as wheat and grapes), causing losses in crop yield, which are costly to the agricultural economy and threaten food security. Azole antifungals are the treatment of choice; however, resistance has arisen against these compounds, which could lead to devastating consequences. Therefore, it is important to understand how these fungicides are used and how the resistance arises in order to tackle the problem fully. Here, we give an overview of the problem and discuss the mechanisms that mediate azole resistance in agriculture (point mutations in the CYP51 amino acid sequence, overexpression of the CYP51 enzyme and overexpression of genes encoding efflux pump proteins). © 2015 Society of Chemical Industry.

Pharmacophore-based virtual screening and experimental validation of novel inhibitors against cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase

Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening of novel inhibitors that can combat harmful algal blooms. In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from the SPECs database were selected by using a pharmacophore-based virtual screening strategy. Most of the compounds tested exhibited moderate inhibitory activities (IC50 = 20.7-176.9 μM) against cy-FBP/SBPase. Compound 2 and its analogues 10 and 11 exhibited strong inhibitory activities, with IC50 values of 20.7, 13.4, and 19.0 μM against cy-FBP/SBPase in vitro and EC50 values of 12.3, 10.9, and 2.9 ppm against cyanobacteria Synechocystis PCC6803 in vivo, respectively. The compound 10 was selected in order to perform a refined docking study to investigate the rational binding mode of inhibitors with cy-FBP/SBPase. Furthermore, possible interactions of the residues with inhibitors were examined by site-directed mutagenesis, enzymatic assays, and fluorescence spectral analyses. The results provide insight into the binding mode between the inhibitors and the substrate binding pocket. The observed theoretical and experimental results are in concert, indicating that the modeling strategies and screening methods employed are appropriate to search for novel lead compounds having both structural diversity and high inhibitory activity against cy-FBP/SBPase.

Structural and biochemical characterization of fructose-1,6/sedoheptulose-1,7-bisphosphatase from the cyanobacterium Synechocystis strain 6803

Cyanobacterial fructose-1,6/sedoheptulose-1,7-bisphosphatase (cy-FBP/SBPase) plays a vital role in gluconeogenesis and in the photosynthetic carbon reduction pathway, and is thus a potential enzymatic target for inhibition of harmful cyanobacterial blooms. Here, we describe the crystal structure of cy-FBP/SBPase in complex with AMP and fructose-1,6-bisphosphate (FBP). The allosteric inhibitor AMP and the substrate FBP exhibit an unusual binding mode when in complex with cy-FBP/SBPase. Binding mode analysis suggested that AMP bound to the allosteric sites near the interface across the up/down subunit pairs C1C4 and C2C3 in the center of the tetramer, while FBP binds opposite to the interface between the horizontal subunit pairs C1C2 or C3C4. We identified a series of residues important for FBP and AMP binding, and suggest formation of a disulfide linkage between Cys75 and Cys99. Further analysis indicates that cy-FBP/SBPase may be regulated through ligand binding and alteration of the structure of the enzyme complex. The interactions between ligands and cy-FBP/SBPase are different from those of ligand-bound structures of other FBPase family members, and thus provide new insight into the molecular mechanisms of structure and catalysis of cy-FBP/SBPase. Our studies provide insight into the evolution of this enzyme family, and may help in the design of inhibitors aimed at preventing toxic cyanobacterial blooms.

Structure-based design and synthesis of novel dual-target inhibitors against cyanobacterial fructose-1,6-bisphosphate aldolase and fructose-1,6-bisphosphatase

Cyanobacteria class II fructose-1,6-bisphoshate aldolase (Cy-FBA-II) and cyanobacteria fructose-1,6-bisphosphatase (Cy-FBPase) are two neighboring key regulatory enzymes in the Calvin cycle of the cyanobacteria photosynthesis system. Each of them might be taken as a potential target for designing novel inhibitors to chemically control harmful algal blooms (HABs). In the present paper, a series of novel inhibitors were rationally designed, synthesized, and optimized based upon the structural and interactional information of both Cy-FBA-II and Cy-FBPase, and their inhibitory activities were examined in vitro and in vivo. The experimental results showed that compounds L19e-L19g exhibited moderate inhibitory activities (IC50 = 28.1-103.2 μM) against both Cy-FBA-II and Cy-FBPase; compounds L19a-L19d, L19h, L20a-L20d exhibited high Cy-FBA-II inhibitory activities (IC50 = 2.3-16.9 μM) and moderate Cy-FBPase inhibitory activities (IC50 = 31.5-141.2 μM); however, compounds L20e-L20h could potently inhibit both Cy-FBA-II and Cy-FBPase with IC50 values less than 30 μM, which demonstrated more or less dual-target inhibitor's feature. Moreover, most of them exhibited potent algicide activity (EC50 = 0.8-22.3 ppm) against cyanobacteria Synechocystis sp. PCC 6803.

Homology modeling a fast tool for drug discovery: current perspectives

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.

Study on the interaction between cyanobacteria FBP/SBPase and metal ions

Fructose-1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) is a potential important target enzyme for finding inhibitors to solve harmful algal bloom. In this paper, the interactions between FBP/SBPase and metal ions were studied by enzyme activity analysis, fluorescence and molecular modeling method. The enzyme activity analysis showed that FBP/SBPase can be activated by Mg2+ or Mn2+ but cannot be activated by Ca2+ or Zn2+. Spectroscopic analysis of emission quenching showed that quenching mechanism of FBP/SBPase with Mg2+ or Mn2+ was static quenching mechanism while that of Ca2+ or Zn2+ was dynamic quenching process. Hydrogen bonds and van der Waals interaction might be the predominant intermolecular forces in stabilizing FBP/SBPase-Mg2+ while hydrophobic forces were the predominant intermolecular forces in stabilizing FBP/SBPase-Mn2+. Microenvironment and conformation of FBP/SBPase were changed in binding reaction. The effect of metal ions and important amino acid residues on FBP/SBPase-metal ion complex was also discussed by molecular modeling study.

Homology modeling and screening of new 14α-demethylase inhibitor (DMI) fungicides based on optimized expression of CYP51 from Ustilago maydis in Escherichia coli

Ustilago maydis infection is a serious disease affecting corn crops worldwide. Sterol 14α-demethylase (CYP51) is one of the key enzymes of sterol biosynthesis and an effective target of antifungal drugs. To further study the interaction between CYP51 and drugs and exploit more specific 14α-demethylase inhibitor (DMI) fungicides for U. maydis, in this study homology modeling of CYP51 from U. maydis (UmCYP51) templated as the eukaryotic orthologues (the human CYP51) and screening of new DMI fungicides based on optimized expression were carried out for the first time. In addition, XF-113 and ZST-4 were screened by analyzing the spectral characteristics between the purified UmCYP51-35 and fungicides. These results provide a theoretical basis and new ideas for efficient design and development of new antifungal drugs.

Optimised expression and spectral analysis of the target enzyme CYP51 from Penicillium digitatum with possible new DMI fungicides

BACKGROUND

Sterol 14α-demethylase (CYP51), a key target of azole (DMI) fungicides, can be expressed in both prokaryotes and eukaryotes. Green mould of citrus, caused by Penicillium digitatum (Pers.) Sacc., is a serious post-harvest disease. To develop specific and more effective fungicides against this disease, the characteristics of the interaction between sterol 14α-demethylase from P. digitatum (PdCYP51) and possible new fungicides were analysed. The cyp51 gene of P. digitatum was cloned and expressed under different conditions in Escherichia coli (Mig.) Cast. & Chalm., and the binding spectra of PdCYP51 were explored by the addition of two commercial azoles and four new nitrogen compounds.

RESULTS

The yield of soluble protein (PdCYP51) was largest when expressed in Rosetta (DE3) induced by 0.5 mM IPTG for 8 h at 30 °C. Compound B (7-methoxy-2H-benzo[b][1,4]thiazine-3-amine) showed the strongest binding activity of the four new nitrogen compounds, with a K(d) value of 0.268 µM. The K(d) values of the six compounds were significantly correlated with their EC(50) values.

CONCLUSION

The spectral analysis and bioassay results could be used to screen the new chemical entities effectively. Compound B, selected by virtual screening from a commercial chemical library, is a candidate for a new DMI fungicide. These results provide a theoretical basis and new ideas for efficient design and development of new antifungal agents.