Efficacy of proton pump inhibitor drugs against Plasmodium falciparum in vitro and their probable pharmacophores

Repurposing of rabeprazole as an anti-Trypanosoma cruzi drug that targets cellular triosephosphate isomerase

Trypanosoma cruzi is the causative agent of American trypanosomiasis, which mainly affects populations in Latin America. Benznidazole is used to control the disease, with severe effects in patients receiving this chemotherapy. Previous studies have demonstrated the inhibition of triosephosphate isomerase from T. cruzi, but cellular enzyme inhibition has yet to be established. This study demonstrates that rabeprazole inhibits both cell viability and triosephosphate isomerase activity in T. cruzi epimastigotes. Our results show that rabeprazole has an IC50 of 0.4 µM, which is 14.5 times more effective than benznidazole. Additionally, we observed increased levels of methyl-glyoxal and advanced glycation end products after the inhibition of cellular triosephosphate isomerase by rabeprazole. Finally, we demonstrate that the inactivation mechanisms of rabeprazole on triosephosphate isomerase of T. cruzi can be achieved through the derivatization of three of its four cysteine residues. These results indicate that rabeprazole is a promising candidate against American trypanosomiasis.

An elegant approach for selective synthesis of 2-substituted benzimidazoles at room temperature using Ag nanoparticles as an activator: effect of solvent on the selectivity

An expedient, competent, and green protocol was developed for the selective synthesis of 2-substituted benzimidazole by the condensation of 1,2-diaminobenzene and various aldehydes, including aromatic, heteroaromatic, and aliphatic aldehydes, in methanol and water (1:1) as reaction media in the presence of Ag nanoparticles in a one pot operation at room temperature. The selectivity of the protocol for obtaining 2-substituted benzimidazole is highly dependent on the ratios of methanol and water used, as well as the reaction temperature. The present protocol exhibits several advantages, such as high yield, short reaction time, high selectivity, and no side reaction, and it works at room temperature, which makes this methodology green, providing a practical input to the existing procedures available for the synthesis of 2-substituted benzimidazole derivatives.

Repurposing Lansoprazole and Posaconazole to treat leishmaniasis: Integration of in vitro testing, pharmacological corroboration, and mechanisms of action

Leishmaniasis remains a serious public health problem in many tropical regions of the world. Among neglected tropical diseases, the mortality rate of leishmaniasis is second only to malaria. All currently approved therapeutics have toxic side effects and face rapidly increasing resistance. To identify existing drugs with antileishmanial activity and predict the mechanism of action, we designed a drug-discovery pipeline utilizing both in-silico and in-vitro methods. First, we screened compounds from the Selleckchem Bio-Active Compound Library containing ~1622 FDA-approved drugs and narrowed these down to 96 candidates based on data mining for possible anti-parasitic properties. Next, we completed preliminary in-vitro testing of compounds against Leishmania amastigotes and selected the most promising active compounds, Lansoprazole and Posaconazole. We identified possible Leishmania drug targets of Lansoprazole and Posaconazole using several available servers. Our in-silico screen identified likely Lansoprazole targets as the closely related calcium-transporting ATPases (LdBPK_352080.1, LdBPK_040010.1, and LdBPK_170660.1), and the Posaconazole target as lanosterol 14-alpha-demethylase (LdBPK_111100.1). Further validation showed LdBPK_352080.1 to be the most plausible target based on induced-fit docking followed by long (100ns) MD simulations to confirm the stability of the docked complexes. We present a likely ion channel-based mechanism of action of Lansoprazole against Leishmania calcium-transporting ATPases, which are essential for parasite metabolism and infectivity. The LdBPK_111100.1 interaction with Posaconazole is very similar to the known fungal orthologue. Herein, we present two novel anti-leishmanial agents, Posaconazole and Lansoprazole, already approved by the FDA for different indications and propose plausible mechanisms of action for their antileishmanial activity.

Anti-infective properties of proton pump inhibitors: perspectives

Infectious diseases are among the main causes of morbidity and mortality today. In facing this crisis, the development of new drug options and combat strategies is necessary. In this sense, drug repositioning or drug redirection has emerged for the faster identification of effective drugs. In this “Commentary,” the anti-infective properties of the class of proton pump inhibitors (PPIs) are emphasized. Studies report activities against bacterial, fungal, parasitic, and viral agents. In addition, we have provided in a table a summary of the specific characteristics of PPIs and some of their anti-infective activities.

cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data

Traditional drug discovery methods focus on optimizing the efficacy of a drug against a single biological target of interest for a specific disease. However, evidence supports the multitarget theory, i.e., drugs work by exerting their therapeutic effects via interaction with multiple biological targets, which have multiple phenotypic effects. Analytics of drug-protein interactions on a large proteomic scale provides insight into disease systems while also allowing for prediction of putative therapeutics against specific indications. We present a Python package for analysis of drug-proteome and drug-disease relationships implementing the Computational Analysis of Novel Drug Opportunities (CANDO) platform. The CANDO package allows for rapid drug similarity assessment, most notably via an in-house interaction scoring protocol where billions of drug-protein interactions are rapidly scored and the similarity of drug-proteome interaction signatures is calculated. The package also implements a variety of benchmarking protocols for shotgun drug discovery and repurposing, i.e., to determine how every known drug is related to every other in the context of the indications/diseases for which they are approved. Drug predictions are generated through consensus scoring of the most similar compounds to drugs known to treat a particular indication. Support for comparing and ranking novel chemical entities, as well as machine learning modules for both benchmarking and putative drug candidate prediction is also available. The CANDO Python package is available on GitHub at https://github.com/ram-compbio/CANDO, through the Conda Python package installer, and at http://compbio.org/software/.

Determination of chemical shift anisotropy tensor and molecular correlation time of proton pump inhibitor omeprazole by solid state NMR measurements

The correlation between the structure and dynamics of omeprazole is portrayed by extracting CSA parameters through the ¹³C 2DPASS CP-MAS SSNMR experiment, site specific spin–lattice relaxation time by Torchia CP experiment, and calculation of the molecular correlation time.

Assessment of the potential therapeutic effects of omeprazole in Schistosoma mansoni infected mice

Schistosomiasis is a neglected chronic parasitic disease with a significant lasting morbidity. Currently, praziquantel (PZQ) is the most efficient drug for schistosomiasis worldwide. However, the possibility of the occurrence of resistance to PZQ is increasing. Therefore, there is a vital need to find new antischistosomal drugs or to increase the efficacy of the existing ones. Omeprazole is a proton pump inhibitor which is reported to have antiparasitic properties. Thus, the aim of this study was to assess the potential therapeutic effects of omeprazole in experimental Schistosoma mansoni infection either alone or in combination with PZQ. For this aim, 80 laboratory bred mice were divided into 3 groups; uninfected control, infected untreated control, and infected and treated at tenth week P.I. The last group was divided into three subgroups that received either PZQ alone, omeprazole alone, or both drugs. The effectiveness of treatment was assessed by adult worm counts, liver egg count, scanning electron microscopy of adult worms, histopathological, and immunohistochemical (GFAP) examination. There was significant reduction of adult worm counts, liver egg counts, size, diameter of hepatic granulomas, hepatic fibrosis, and GFAP expression in the group that received combined treatment as compared to PZQ group. Moreover, the tegumental changes were more evident in the group that received combined treatment. In conclusion, the administration of omeprazole with PZQ improved the efficacy of PZQ in the treatment of Schistosomiasis mansoni.

Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease

The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.

A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India

A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.

Synergy of Omeprazole and Praziquantel In Vitro Treatment against Schistosoma mansoni Adult Worms

Background

Treatment and morbidity control of schistosomiasis relies on a single drug, praziquantel (PZQ), and the selection of resistant worms under repeated treatment is a concern. Therefore, there is a pressing need to understand the molecular effects of PZQ on schistosomes and to investigate alternative or synergistic drugs against schistosomiasis.

Methodology

We used a custom-designed Schistosoma mansoni expression microarray to explore the effects of sublethal doses of PZQ on large-scale gene expression of adult paired males and females and unpaired mature females. We also assessed the efficacy of PZQ, omeprazole (OMP) or their combination against S. mansoni adult worms with a survival in vitro assay.

Principal Findings

We identified sets of genes that were affected by PZQ in paired and unpaired mature females, however with opposite gene expression patterns (up-regulated in paired and down-regulated in unpaired mature females), indicating that PZQ effects are heavily influenced by the mating status. We also identified genes that were similarly affected by PZQ in males and females. Functional analyses of gene interaction networks were performed with parasite genes that were differentially expressed upon PZQ treatment, searching for proteins encoded by these genes whose human homologs are targets of different drugs used for other diseases. Based on these results, OMP, a widely prescribed proton pump inhibitor known to target the ATP1A2 gene product, was chosen and tested. Sublethal doses of PZQ combined with OMP significantly increased worm mortality in vitro when compared with PZQ or OMP alone, thus evidencing a synergistic effect.

Conclusions

Functional analysis of gene interaction networks is an important approach that can point to possible novel synergistic drug candidates. We demonstrated the potential of this strategy by showing that PZQ in combination with OMP displayed increased efficiency against S. mansoni adult worms in vitro when compared with either drug alone.

Schistosomiasis causes severe health problems in endemic areas of Africa, Southeast Asia, and Central and South America. Praziquantel is the drug of choice for treatment of at-risk populations; however, evolution of resistant worms under repeated treatment is of great concern. Combining praziquantel with another drug could not only increase efficacy of praziquantel, but also eventually hamper development of drug resistance. Our study reports the global praziquantel-induced transcriptional changes of Schistosoma mansoni adult worms in vitro, in the context of the mature female mating status (paired or unpaired). We identified sets of genes that were differentially affected in paired or unpaired mature females; we also identified genes that were similarly affected in males and females. Aiming to find possible new candidates to be tested as synergistic drugs, we used functional analysis of gene interaction networks to identify parasite genes whose expression was affected by praziquantel, and encode proteins whose human homologs are targets of different drugs already used to treat other diseases. This analysis suggested omeprazole, a widely prescribed drug, as a potential partner for praziquantel in a combination treatment. Finally, we demonstrated that this praziquantel-omeprazole combination resulted in increased worm lethality in vitro when compared with praziquantel or omeprazole alone.

Hematin loses its membranotropic activity upon oligomerization into malaria pigment

Malaria is an infectious disease caused by Plasmodium type parasites transmitted by the bites of infected female anopheles mosquitoes. The malaria parasite multiplies in red blood cells where it degrades hemoglobin. This degradation of hemoglobin proteins releases hematin, an iron-containing porphyrin, which provokes membrane disruption and lysis. The malaria parasite blocks hematin-induced lysis by biocrystallization, a process that converts hematin into insoluble and chemically inert crystals. Hematin molecules are especially prone to self-assembly as dimers, oligomers and aggregates depending on environmental conditions (pH, solvent, temperature, concentration, ionic strength). Considering the different forms of hematin-based assemblies, it is still unclear which are the ones able to interact with membranes. We have prepared hematin under different conditions to form hematin-based assemblies and to measure their ability to interact and to disorganize membranes. Our results show that different forms of hematin molecules are able to penetrate lipid membranes. Interestingly, this membrane activity is spontaneously inhibited at acidic pH and it can be restored under neutral pH. By contrast, the oligomers of β-hematin were found to be completely harmless toward lipid membranes. Finally, the AFM visualization of hematin interaction with supported lipid bilayers showed for the first time its preferential interaction with defaults in membranes, at the boundaries between two distinct lipid phases. The superficial adsorption of aggregates on membranes and the absence of effect due to oligomers were also confirmed with AFM.

Enhanced dissolution and stability of lansoprazole by cyclodextrin inclusion complexation: preparation, characterization, and molecular modeling

In this study, lansoprazole (LSP)/cyclodextrin (CD) inclusion complexes were prepared using a fluid bed coating technique, with β-cyclodextrin (β-CD) and 2-hydroxypropyl-β-cyclodextrin (HPCD) as the host molecules, respectively, to simultaneously improve the dissolution and stability of LSP. The dissolution rate and stability of LSP was dramatically enhanced by inclusion complexation regardless of CD type. LSP/HPCD inclusion complex was more stable under illumination than LSP/β-CD inclusion complex. Differential scanning calorimetry and powder X-ray diffractometry proved the absence of crystallinity in both LSP/CD inclusion complexes. Fourier transform infrared spectroscopy together with molecular modeling indicated that the benzimidazole of LSP was included in the cavity of both CDs, while LSP was more deeply included in HPCD than β-CD. The enhanced photostability was due to the inclusion of the sulfinyl moiety into the HPCD cavity. CD inclusion complexation could improve the dissolution and stability of LSP.

Liver-stage malaria parasites vulnerable to diverse chemical scaffolds

Human malaria infection begins with a one-time asymptomatic liver stage followed by a cyclic symptomatic blood stage. All high-throughput malaria drug discovery efforts have focused on the cyclic blood stage, which has limited potential for the prophylaxis, transmission blocking, and eradication efforts that will be needed in the future. To address these unmet needs, a high-throughput phenotypic liver-stage Plasmodium parasite screen was developed to systematically identify molecules with liver-stage efficacy. The screen recapitulates liver-stage infection by isolating luciferase-expressing Plasmodium berghei parasites directly from the salivary glands of infected mosquitoes, adding them to confluent human liver cells in 384-well plates, and measuring luciferase activity after a suitable incubation period. Screening 5,375 known bioactive compounds identified 37 liver-stage malaria inhibitors with diverse modes of action, as shown by inhibition time course experiments. Further analysis of the hits in the Food and Drug Administration-approved drug subset revealed compounds that seem to act specifically on the liver stage of infection, suggesting that this phase of the parasite's life cycle presents a promising area for new drug discovery. Notably, many active compounds in this screen have molecular structures and putative targets distinctly different from those of known antimalarial agents.

Quantitative bioactivity prediction and pharmacophore identification for benzotriazine derivatives using the electron conformational-genetic algorithm in QSAR

The electron conformational-genetic algorithm (EC-GA), a sophisticated hybrid approach combining the GA and EC methods, has been employed for a 4D-QSAR procedure to identify the pharmacophore for benzotriazines as sarcoma inhibitors and for quantitative prediction of activity. The calculated geometry and electronic structure parameters of every atom and bond of each molecule are arranged in a matrix described as the electron-conformational matrix of contiguity (ECMC). By comparing the ECMC of one of the most active compounds with other ECMCs we were able to obtain the features of the pharmacophore responsible for the activity, as submatrices of the template known as electron conformational submatrices of activity. The GA was used to select the most important descriptors and to predict the theoretical activity of training and test sets. The predictivity of the model was internally validated. The best QSAR model was selected, having r² = 0.9008, standard error = 0.0510 and cross-validated squared correlation coefficient, q² = 0.8192.

A review of rabeprazole in the treatment of acid-related diseases

Rabeprazole is a proton pump inhibitor. Pharmacodynamic data show rabeprazole can achieve optimal acid suppression since the first administration and can maintain this advantage in the following days of therapy. Moreover, rabeprazole has the highest pKa (~ 5.0, the pH at which a drug becomes 50% protonated), and hence the molecule can be activated at higher pH levels much faster than other PPIs. Due to its peculiar catabolic pathway, ie, a prevalent metabolism through a non-enzymatic pathway, rabeprazole is less susceptible to the influence of genetic polymorphisms for CYP2C19, resulting in minor influences on its pharmacokinetics and pharmacodynamics. In terms of clinical efficacy, rabeprazole 20 mg uid or 10 mg bid produced healing rates at 8 weeks similar to those obtained with omeprazole 20 mg uid in erosive esophagitis patients, and in NERD patients doses of 10 or 20 mg are equivalent and both are better than placebo at 2 and 4 weeks. To prevent symptomatic relapse, on-demand strategy with rabeprazole 10 mg daily appears to be ideal, due to its rapidity of onset; results on NERD patients have documented its superiority over placebo. Continuous treatment, however, up to 5 years, seems to achieve better results than on-demand therapy, particularly in patients with esophagitis. It is debated whether in the latter halved doses (10 mg) are really equivalent to full dose (20 mg). Rabeprazole has been used with success in the treatment of some atypical GERD manifestations, such as dysphagia associated with GERD, GERD-related asthma and chest-pain, and in the therapy of Barrett's esophagus. Finally, rabeprazole achieves similar Helicobacter pylori eradication rates compared with omeprazole and lansoprazole when co-administrated with low or high doses of antibiotics (amoxicillin and clarithromycin). In addition, low doses of rabeprazole (10 mg/bid) may be effective in eradicating the pathogen.

Functional complementation of the yeast P-type H-ATPase, PMA1, by the Pneumocystis carinii P-type H-ATPase, PCA1

The opportunistic fungus Pneumocystis is the etiologic agent of an interstitial plasma cell pneumonia that primarily afflicts immunocompromised individuals. Like other fungi Pneumocystis maintains a H(+) plasma membrane gradient to drive nutrient uptake and regulates intracellular pH by ATP-dependent proton efflux. Previously, we identified a Pneumocystis gene, PCA1, whose predicted protein product was homologous to fungal proton pumps. In this study, we show by functional complementation in a Saccharomyces strain whose endogenous PMA1 proton pump activity is repressed that the Pneumocystis PCA1 encodes a H(+)-ATPase. The properties of PCA1 characterized in this system closely resemble those of yeast PMA1. Yeast expressing PCA1 grow at low pH and are able to acidify the external media. Maximal enzyme activity (V(max)) and efficiency of substrate utilization (K(m)) in plasma membranes were nearly identical for PCA1 and PMA1. PCA1 contains an inhibitory COOH-terminal domain; removal of the final 40 amino acids significantly increased V(max) and growth at pH 6.5. PCA1 activity was inhibited by proton pump inhibitors omeprazole and lansoprazole, but was unaffected by H(+)/K(+)-ATPase inhibitor SCH28080. Thus, H(+) homeostasis in Pneumocystis is likely regulated as in other fungi. This work also establishes a system for screening PCA1 inhibitors to identify new anti-Pneumocystis agents.

A COOH-terminal domain regulates the activity of Leishmania proton pumps LDH1A and LDH1B

Leishmania donovani requires actively transporting proton efflux pumps to survive the acidic environment of macrophage phagolysosomal vacuoles and to maintain an electrogenic H(+) gradient for nutrient uptake. The L. donovani genome contains a differentially expressed pair of genes, LDH1A and LDH1B, with homology to yeast H(+)-ATPases that are 98% identical in sequence with amino acid differences concentrated at the COOH-terminus (15 of last 37 differ), a region implicated in regulation of yeast and plant proton pumps. Functional complementation of a Saccharomyces cerevisiae strain deficient in endogenous H(+)-ATPase activity, support of yeast growth at low pH, and ability to acidify media demonstrate that LDH1A and LDH1B encode proton pumps. LDH1A and LDH1B encode a COOH-terminal autoinhibitory domain as COOH-truncated peptides support increased rates of growth in yeast, enhanced media acidification, increased enzyme activity (V(max)) and decreased K(m). This regulatory domain mediates differing function properties; LDH1A, but not LDH1B, supports yeast growth at pH 3 and LDH1A shows a greater ability to acidify media. Deletion of the last eight amino acids from LDH1B permits growth at pH 3 and increases media acidification, swapping of the COOH-tails between LDH1A and LDH1B results in LDH1A (with LDH1B tail) unable to support yeast growth at pH 3 and LDH1B (with LDH1A tail) now able to support growth at pH 3. Replacement of the COOH-terminal eight amino acids of LDH1B with those from LDH1A also confers the ability to support growth at pH 3. The complementation system for the Leishmania proton pumps in yeast described here provides a means to dissect the functional properties of the two isoforms, a convenient supply of protein for structural analysis and a model amenable to screening proton pump inhibitors for potential anti-leishmanial therapeutics.

In vitro antimalarial activity of flavonoid derivatives dehydrosilybin and 8-(1;1)-DMA-kaempferide

Multidrug-resistant Plasmodium falciparum strains are an increasing problem in endemic areas and are partly responsible for the worsening malaria situation around the world. New cheap and effective compounds active in combination with available drug in the field are urgently needed. The aim of this work was to explore the potential antiplasmodial effect of flavonoid derivatives on parasites growth in vitro. In vitro antiplasmodial activity of dehydrosilybin and 8-(1;1)-DMA-kaempferide has been evaluated by real time PCR for five P. falciparum strains. Both revealed significative antimalarial activity against the different strains. Since this drug family has been largely used and well-tolerated in humans, flavonoid derivatives could be in the near future associated with already available drugs in order to delay the spread of P. falciparum resistance.