Repositioning of an existing drug for the neglected tropical disease Onchocerciasis

DReAmocracy: A Method to Capitalise on Prior Drug Discovery Efforts to Highlight Candidate Drugs for Repurposing

In the area of drug research, several computational drug repurposing studies have highlighted candidate repurposed drugs, as well as clinical trial studies that have tested/are testing drugs in different phases. To the best of our knowledge, the aggregation of the proposed lists of drugs by previous studies has not been extensively exploited towards generating a dynamic reference matrix with enhanced resolution. To fill this knowledge gap, we performed weight-modulated majority voting of the modes of action, initial indications and targeted pathways of the drugs in a well-known repository, namely the Drug Repurposing Hub. Our method, DReAmocracy, exploits this pile of information and creates frequency tables and, finally, a disease suitability score for each drug from the selected library. As a testbed, we applied this method to a group of neurodegenerative diseases (Alzheimer's, Parkinson's, Huntington's disease and Multiple Sclerosis). A super-reference table with drug suitability scores has been created for all four neurodegenerative diseases and can be queried for any drug candidate against them. Top-scored drugs for Alzheimer's Disease include agomelatine, mirtazapine and vortioxetine; for Parkinson's Disease, they include apomorphine, pramipexole and lisuride; for Huntington's, they include chlorpromazine, fluphenazine and perphenazine; and for Multiple Sclerosis, they include zonisamide, disopyramide and priralfimide. Overall, DReAmocracy is a methodology that focuses on leveraging the existing drug-related experimental and/or computational knowledge rather than a predictive model for drug repurposing, offering a quantified aggregation of existing drug discovery results to (1) reveal trends in selected tracks of drug discovery research with increased resolution that includes modes of action, targeted pathways and initial indications for the investigated drugs and (2) score new candidate drugs for repurposing against a selected disease.

Ion transporter cascade, reactive astrogliosis and cerebrovascular diseases

Cerebrovascular diseases and their sequalae, such as ischemic stroke, chronic cerebral hypoperfusion, and vascular dementia are significant contributors to adult disability and cognitive impairment in the modern world. Astrocytes are an integral part of the neurovascular unit in the CNS and play a pivotal role in CNS homeostasis, including ionic and pH balance, neurotransmission, cerebral blood flow, and metabolism. Astrocytes respond to cerebral insults, inflammation, and diseases through unique molecular, morphological, and functional changes, collectively known as reactive astrogliosis. The function of reactive astrocytes has been a subject of debate. Initially, astrocytes were thought to primarily play a supportive role in maintaining the structure and function of the nervous system. However, recent studies suggest that reactive astrocytes may have both beneficial and detrimental effects. For example, in chronic cerebral hypoperfusion, reactive astrocytes can cause oligodendrocyte death and demyelination. In this review, we will summarize the (1) roles of ion transporter cascade in reactive astrogliosis, (2) role of reactive astrocytes in vascular dementia and related dementias, and (3) potential therapeutic approaches for dementing disorders targeting reactive astrocytes. Understanding the relationship between ion transporter cascade, reactive astrogliosis, and cerebrovascular diseases may reveal mechanisms and targets for the development of therapies for brain diseases associated with reactive astrogliosis.

A novel efficient drug repurposing framework through drug-disease association data integration using convolutional neural networks

Drug repurposing is an exciting field of research toward recognizing a new FDA-approved drug target for the treatment of a specific disease. It has received extensive attention regarding the tedious, time-consuming, and highly expensive procedure with a high risk of failure of new drug discovery. Data-driven approaches are an important class of methods that have been introduced for identifying a candidate drug against a target disease. In the present study, a model is proposed illustrating the integration of drug-disease association data for drug repurposing using a deep neural network. The model, so-called IDDI-DNN, primarily constructs similarity matrices for drug-related properties (three matrices), disease-related properties (two matrices), and drug-disease associations (one matrix). Then, these matrices are integrated into a unique matrix through a two-step procedure benefiting from the similarity network fusion method. The model uses a constructed matrix for the prediction of novel and unknown drug-disease associations through a convolutional neural network. The proposed model was evaluated comparatively using two different datasets including the gold standard dataset and DNdataset. Comparing the results of evaluations indicates that IDDI-DNN outperforms other state-of-the-art methods concerning prediction accuracy.

Current status of usage of ivermectin in the management of COVID

The antibacterial, antiviral, and anticancer properties of ivermectin make it a wonder drug with a wide range of possible applications. It works against a variety of microorganisms, including viruses. Ivermectin has a wide range of antiviral effects, according to in vivo research in animal models. Because ivermectin is involved in a range of biological processes, it could be a promising therapeutic candidate for viruses such as COVID-19 and other positive-sense single-stranded RNA viruses. The study aims to analyze the awareness about the current status of usage of ivermectin in management of COVID among students studying in a private dental college. A study based on questionnaire was organized among students studying in a private dental college in Tamil Nadu. The subjects were asked a series of structural questions based on the usage of ivermectin in management of COVID. The questionnaire was prepared with 10 questions. 150 individuals completed the questionnaire; all of their answers were tallied in excel and imported into SPSS. For statistical analysis, the Chi-square test was performed. Excel was used to tabulate and enter the data, and the SPSS package software was used to analyze it. The study's threshold for statistical significance was set at P < 0.05. From this study, we found that the students had limited knowledge about the usage of ivermectin for management of COVID. More studies should be conducted to widen the knowledge among the students about the current affairs of the world.

Discovery of novel inhibitors targeting nematode chitinase CeCht1: Virtual screening, biological evaluation, and molecular dynamics simulation

Plant-parasitic nematodes are a main limiting factor for worldwide agriculture. To reduce the global burden of nematode infections, chemical nematicides are still the most effective methods to manage nematodes. With the increasing resistance of nematodes, the development of new anti-nematicides drug is urgent. Nematode chitinases are found to play important roles in various physiological functions, such as larva moulting, hatching from eggshell, and host infection. Inhibition of nematode chitinase is considered a promising strategy for the development of eco-friendly nematicides. In this study, to develop novel nematode chitinase CeCht1 inhibitors, virtual screening of the ZINC database was performed using the pesticide-likeness rules, pharmacophore-based and docking-based approach in turn. Compounds HAU-4 and HAU-7 were identified as potent CeCht1 inhibitors with the IC50 values of 4.2 μM and 10.0 μM, respectively. Moreover, molecular dynamics simulations combined with binding free energy and free energy decomposition calculations were conducted to investigate the basis for the potency of the two inhibitors toward CeCht1. This work gives an insight into the future rational development of novel and potent nematode chitinase inhibitors.

Drug development for onchocerciasis-the past, the present and the future

Onchocerciasis affects predominantly rural communities in Africa, and with small foci in South America and the Yemen. The disease is a major cause of blindness and other significant morbidity and mortality. Control programs have achieved a major impact on the incidence and prevalence of onchocerciasis by interrupting transmission with vector control programs, and treatment with mass drug administration using the microfilaricide ivermectin. Over the last few decades, several microfilaricides have been developed. This initially included diethylcarbamazine, which had significant side effects and is no longer used as such. Ivermectin which is a safe and highly effective microfilaricide and moxidectin which is a longer acting microfilaricide are presently recognized therapies. Suramin was the first effective macrofilaricide but was prohibitively toxic. Certain antibiotics including doxycycline can help eliminate adult worms by targeting its endosymbiont bacteria, Wolbachia pipientis. However, the dosing regimens may make this difficult to use as part of a mass disease control program in endemic areas. It is now widely recognized that treatments that are able to kill or permanently sterilize adult filarial worms should help achieve the elimination of this disease. We summarize in detail the historic drug development in onchocerciasis, including prospective future candidate drugs.

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1

Nematode chitinases play vital roles in various physiological processes, including egg hatching, larva moulting, and reproduction. Small-molecule inhibitors of nematode chitinases have potential applications for controlling nematode pests. On the basis of the crystal structure of CeCht1, a representative chitinase indispensable to the eggshell chitin degradation of the model nematode Caenorhabditis elegans, we have discovered a series of novel inhibitors bearing a (R)-3,4-diphenyl-4,5-dihydropyrrolo[3,4-c]pyrazol-6(2H)-one scaffold by hierarchical virtual screening. The crystal structures of CeCht1 complexed with two of these inhibitors clearly elucidated their interactions with the enzyme active site. Based on the inhibitory mechanism, several analogues with improved inhibitory activities were identified, among which the compound PP28 exhibited the most potent activity with a K_i value of 0.18 μM. This work provides the structural basis for the development of novel nematode chitinase inhibitors.

Crystal Structure and Structure-Based Discovery of Inhibitors of the Nematode Chitinase CeCht1

Nematode chitinases play crucial roles in various processes of the nematode lifecycle, including hatching, molting, and reproduction. Small-molecule inhibitors of nematode chitinases have shown promise for controlling nematode pests. However, the lack of structural information makes it a challenge to develop nematicides targeting nematode chitinases. Here, we report the first crystal structure of a representative nematode chitinase, that of CeCht1 from the model nematode Caenorhabditis elegans, to a 1.7 Å resolution. CeCht1 is a highly conserved chitinase among nematodes, and structural comparison with other chitinases revealed that CeCht1 has a classical TIM-barrel fold with some subtle structural differences in the substrate-binding cleft. Benefiting from the obtained crystal structure, we identified a series of novel inhibitors by hierarchical virtual screening. Analysis of the structure-activity relationships of these compounds provided insight into their interactions with the enzyme active site, which may inform future work in improving the potencies of their inhibitory activities. This work gives an insight into the structural features of nematode chitinases and provides a solid basis for the development of inhibitors.

SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks

BACKGROUND

Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug repositioning plays an instrumental role in optimizing the drug development process compared to the traditional de novo drug discovery process. Advances in the genomics, together with the enormous growth of large-scale publicly available data and the availability of high-performance computing capabilities, have further motivated the development of computational drug repositioning approaches. More recently, the rise of machine learning techniques, together with the availability of powerful computers, has made the area of computational drug repositioning an area of intense activities.

RESULTS

In this study, a novel framework SNF-NN based on deep learning is presented, where novel drug-disease interactions are predicted using drug-related similarity information, disease-related similarity information, and known drug-disease interactions. Heterogeneous similarity information related to drugs and disease is fed to the proposed framework in order to predict novel drug-disease interactions. SNF-NN uses similarity selection, similarity network fusion, and a highly tuned novel neural network model to predict new drug-disease interactions. The robustness of SNF-NN is evaluated by comparing its performance with nine baseline machine learning methods. The proposed framework outperforms all baseline methods ([Formula: see text] = 0.867, and [Formula: see text]=0.876) using stratified 10-fold cross-validation. To further demonstrate the reliability and robustness of SNF-NN, two datasets are used to fairly validate the proposed framework's performance against seven recent state-of-the-art methods for drug-disease interaction prediction. SNF-NN achieves remarkable performance in stratified 10-fold cross-validation with [Formula: see text] ranging from 0.879 to 0.931 and [Formula: see text] from 0.856 to 0.903. Moreover, the efficiency of SNF-NN is verified by validating predicted unknown drug-disease interactions against clinical trials and published studies.

CONCLUSION

In conclusion, computational drug repositioning research can significantly benefit from integrating similarity measures in heterogeneous networks and deep learning models for predicting novel drug-disease interactions. The data and implementation of SNF-NN are available at http://pages.cpsc.ucalgary.ca/ tnjarada/snf-nn.php .

Drug-drug similarity measure and its applications

Drug similarities play an important role in modern biology and medicine, as they help scientists gain deep insights into drugs' therapeutic mechanisms and conduct wet labs that may significantly improve the efficiency of drug research and development. Nowadays, a number of drug-related databases have been constructed, with which many methods have been developed for computing similarities between drugs for studying associations between drugs, human diseases, proteins (drug targets) and more. In this review, firstly, we briefly introduce the publicly available drug-related databases. Secondly, based on different drug features, interaction relationships and multimodal data, we summarize similarity calculation methods in details. Then, we discuss the applications of drug similarities in various biological and medical areas. Finally, we evaluate drug similarity calculation methods with common evaluation metrics to illustrate the important roles of drug similarity measures on different applications.

A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in optimizing the pre-clinical process of developing novel drugs by saving time and cost compared to the traditional de novo drug discovery processes. Since drug repositioning relies on data for existing drugs and diseases the enormous growth of publicly available large-scale biological, biomedical, and electronic health-related data along with the high-performance computing capabilities have accelerated the development of computational drug repositioning approaches. Multidisciplinary researchers and scientists have carried out numerous attempts, with different degrees of efficiency and success, to computationally study the potential of repositioning drugs to identify alternative drug indications. This study reviews recent advancements in the field of computational drug repositioning. First, we highlight different drug repositioning strategies and provide an overview of frequently used resources. Second, we summarize computational approaches that are extensively used in drug repositioning studies. Third, we present different computing and experimental models to validate computational methods. Fourth, we address prospective opportunities, including a few target areas. Finally, we discuss challenges and limitations encountered in computational drug repositioning and conclude with an outline of further research directions.

A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches

A computational technique for predicting the DTIs has now turned out to be an indispensable job during the process of drug finding. It tapers the exploration room for interactions by propounding possible interaction contenders for authentication through experiments of wet-lab which are known for their expensiveness and time consumption. Chemogenomics, an emerging research area focused on the systematic examination of the biological impact of a broad series of minute molecular-weighting ligands on a broad raiment of macromolecular target spots. Additionally, with the advancement in time, the complexity of the algorithms is increasing which may result in the entry of big data technologies like Spark in this field soon. In the presented work, we intend to offer an inclusive idea and realistic evaluation of the computational Drug Target Interaction projection approaches, to perform as a guide and reference for researchers who are carrying out work in a similar direction. Precisely, we first explain the data utilized in computational Drug Target Interaction prediction attempts like this. We then sort and explain the best and most modern techniques for the prediction of DTIs. Then, a realistic assessment is executed to show the projection performance of several illustrative approaches in various situations. Ultimately, we underline possible opportunities for additional improvement of Drug Target Interaction projection enactment and also linked study objectives.

Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 2. Ketone Linked Analogs

The optimization of a series of benzimidazole–benzoxaborole hybrid molecules linked via a ketone that exhibit good activity against Onchocerca volvulus, a filarial nematode responsible for the disease onchocerciasis, also known as river blindness, is described. The lead identified in this series, 21 (AN15470), was found to have acceptable pharmacokinetic properties to enable an evaluation following oral dosing in an animal model of onchocerciasis. Compound 21was effective in killing worms implanted in Mongolian gerbils when dosed orally as a suspension at 100 mg/kg/day for 14 days but not when dosed orally at 100 mg/kg/day for 7 days.

Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 1. Amide Linked Analogs

A series of benzimidazole–benzoxaborole hybrid molecules linked via an amide linker are described that exhibit good in vitro activity against Onchocerca volvulus, a filarial nematode responsible for the disease onchocerciasis, also known as river blindness. The lead identified in this series, 8a (AN8799), was found to have acceptable pharmacokinetic properties to enable evaluation in animal models of human filariasis. Compound 8a was effective in killing Brugia malayi, B. pahangi, and Litomosoides sigmodontis worms present in Mongolian gerbils when dosed subcutaneously as a suspension at 100 mg/kg/day for 14 days but not when dosed orally at 100 mg/kg/day for 28 days. The measurement of plasma levels of 8a at the end of the dosing period and at the time of sacrifice revealed an interesting dependence of activity on the extended exposure for both 8a and the positive control, flubendazole.

Evidence of nuclear transport mechanisms in the protozoan parasite Giardia lamblia

Nuclear-cytoplasmic trafficking of proteins is a highly regulated process that modulates multiple biological processes in eukaryotic cells. In Giardia lamblia, shuttling has been described from the cytoplasm to nuclei of proteins during the biological cell cycle of the parasite. This suggests that a mechanism of nucleocytoplasmic transport is present and functional in G. lamblia. By means of computational biology analyses, we found that there are only two genes for nuclear transport in this parasite, named Importin α and Importin β. When these transporters were overexpressed, both localized close to the nuclear envelope, and no change was observed in trophozoite growth rate. However, during the encystation process, both transporters induced an increase in the number of cysts produced. Importazole and Ivermectin, two known specific inhibitors of importins, separately influenced the encysting process by inducing an arrest in the trophozoite stage that prevents the production of cysts. This effect was more noticeable when Ivermectin, an anti-parasitic drug, was used. Finally, we tested whether the enzyme arginine deiminase, which shuttles from the cytoplasm to the nuclei during encystation, was influenced by these transporters. We found that treatment with each of the inhibitors abrogates arginine deiminase nuclear translocation and favors perinuclear localization. This suggests that Importin α and Importin β are key transporters during the encystation process and are involved, at least, in the transport of arginine deiminase into the nuclei. Considering the effect produced by Ivermectin during growth and encystation, we postulate that this drug could be used to treat giardiasis.

Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition

Small-molecule inhibitors of insect chitinases have potential applications for controlling insect pests. Insect group II chitinase (ChtII) is the most important chitinase in insects and functions throughout all developmental stages. However, the possibility of inhibiting ChtII by small molecules has not been explored yet. Here, we report the structural characteristics of four molecules that exhibited similar levels of inhibitory activity against OfChtII, a group II chitinase from the agricultural pest Asian corn borer Ostrinia furnacalis These inhibitors were chitooctaose ((GlcN)₈), dipyrido-pyrimidine derivative (DP), piperidine-thienopyridine derivative (PT), and naphthalimide derivative (NI). The crystal structures of the OfChtII catalytic domain complexed with each of the four inhibitors at 1.4-2.0 Å resolutions suggested they all exhibit similar binding modes within the substrate-binding cleft; specifically, two hydrophobic groups of the inhibitor interact with +1/+2 tryptophan and a -1 hydrophobic pocket. The structure of the (GlcN)₈ complex surprisingly revealed that the oligosaccharide chain of the inhibitor is orientated in the opposite direction to that previously observed in complexes with other chitinases. Injection of the inhibitors into 4th instar O. furnacalis larvae led to defects in development and pupation. The results of this study provide insights into a general mechanistic principle that confers inhibitory activity against ChtII, which could facilitate rational design of agrochemicals that target ecdysis of insect pests.

Development of a preliminary in vitro drug screening assay based on a newly established culturing system for pre-adult fifth-stage Onchocerca volvulus worms

BACKGROUND

The human filarial parasite Onchocerca volvulus is the causative agent of onchocerciasis (river blindness). It causes blindness in 270,000 individuals with an additional 6.5 million suffering from severe skin pathologies. Current international control programs focus on the reduction of microfilaridermia by annually administering ivermectin for more than 20 years with the ultimate goal of blocking of transmission. The adult worms of O. volvulus can live within nodules for over 15 years and actively release microfilariae for the majority of their lifespan. Therefore, protracted treatment courses of ivermectin are required to block transmission and eventually eliminate the disease. To shorten the time to elimination of this disease, drugs that successfully target macrofilariae (adult parasites) are needed. Unfortunately, there is no small animal model for the infection that could be used for discovery and screening of drugs against adult O. volvulus parasites. Here, we present an in vitro culturing system that supports the growth and development of O. volvulus young adult worms from the third-stage (L3) infective stage.

METHODOLOGY/PRINCIPAL FINDINGS

In this study we optimized the culturing system by testing several monolayer cell lines to support worm growth and development. We have shown that the optimized culturing system allows for the growth of the L3 worms to L5 and that the L5 mature into young adult worms. Moreover, these young O. volvulus worms were used in preliminary assays to test putative macrofilaricidal drugs and FDA-approved repurposed drugs.

CONCLUSION

The culture system we have established for O. volvulus young adult worms offers a promising new platform to advance drug discovery against the human filarial parasite, O. volvulus and thus supports the continuous pursuit for effective macrofilaricidal drugs. However, this in vitro culturing system will have to be further validated for reproducibility before it can be rolled out as a drug screen for decision making in macrofilaricide drug development programs.

Nematode Chitin and Application

Plant-parasitic nematode infection is a global problem for agriculture and forestry. There is clearly a need for novel nematicides, because of the pitifully small repertoire of nematicides available and the effectiveness of losing or environmental prohibition of these nematicides. Chitin is the essential component of nematode eggshell and pharynx. The disturbance of chitin synthesis or hydrolysis led to nematode embryonic lethal, laying defective eggs or moulting failure. Thus, the key components in the chitin metabolic process are promising targets for anti-nematode agent's development. In this chapter, we focus on chitin and chitin synthase of nematodes, chitinases and their roles in nematode survival and application of chitin in nematode control.

Impact of five annual rounds of mass drug administration with ivermectin on onchocerciasis in Sierra Leone

BACKGROUND

Onchocerciasis is endemic in 12 of the 14 health districts of Sierra Leone. Good treatment coverage of community-directed treatment with ivermectin was achieved between 2005 and 2009 after the 11-year civil conflict. Sentinel site surveys were conducted in 2010 to evaluate the impact of five annual rounds of ivermectin distribution.

METHODS

In total, 39 sentinel villages from hyper- and meso-endemic areas across the 12 endemic districts were surveyed using skin snips in 2010. Results were analyzed and compared with the baseline data from the same 39 villages.

RESULTS

The average microfilaridermia (MF) prevalence across 39 sentinel villages was 53.10% at baseline. The MF prevalence was higher in older age groups, with the lowest in the age group of 1-9 years (11.00%) and the highest in the age group of 40-49 years (82.31%). Overall mean MF density among the positives was 28.87 microfilariae (mf)/snip, increasing with age with the lowest in the age group of 1-9 years and the highest in the age group of 40-49 years. Males had higher MF prevalence and density than females. In 2010 after five rounds of mass drug administration, the overall MF prevalence decreased by 60.26% from 53.10% to 21.10%; the overall mean MF density among the positives decreased by 71.29% from 28.87 mf/snip to 8.29 mf/snip; and the overall mean MF density among all persons examined decreased by 88.58% from 15.33 mf/snip to 1.75 mf/snip. Ten of 12 endemic districts had > 50% reduction in MF prevalence. Eleven of 12 districts had ≥50% reduction in mean MF density among the positives.

CONCLUSIONS

A significant reduction of onchocerciasis MF prevalence and mean density was recorded in all 12 districts of Sierra Leone after five annual MDAs with effective treatment coverage. The results suggested that the onchocerciasis elimination programme in Sierra Leone was on course to reach the objective of eliminating onchocerciasis in the country by the year 2025. Annual MDA with ivermectin should continue in all 12 districts and further evaluations are needed across the country to assist the NTDP with programme decision making.

Alternative treatment strategies to accelerate the elimination of onchocerciasis

The use of alternative (or complementary) treatment strategies (ATSs) i.e. differing from annual community-directed treatment with ivermectin (CDTI) is required in some African foci to eliminate onchocerciasis by 2025. ATSs include vector control, biannual or pluriannual CDTI, better timing of CDTI, community-directed treatment with combinations of currently available anthelminthics or new drugs, and 'test-and-treat' (TNT) strategies requiring diagnosis of infection and/or contraindications to treatment for decisions on who to treat with what regimen. Two TNT strategies can be considered. Loa-first TNT, designed for loiasis-endemic areas and currently being evaluated using a rapid test (LoaScope), consists of identifying individuals with levels of Loa microfilaremia associated with a risk of post-ivermectin severe adverse events to exclude them from ivermectin treatment and in treating the rest (usually >97%) of the population safely. Oncho-first TNT consists of testing community members for onchocerciasis before giving treatment (currently ivermectin or doxycycline) to those who are infected. The choice of the ATS depends on the prevalences and intensities of infection with Onchocerca volvulus and Loa loa and on the relative cost-effectiveness of the strategies for the given epidemiological situation. Modelling can help select the optimal strategies, but field evaluations to determine the relative cost-effectiveness are urgently needed.

The multitargeted drug ivermectin: from an antiparasitic agent to a repositioned cancer drug

Drug repositioning is a highly studied alternative strategy to discover and develop anticancer drugs. This drug development approach identifies new indications for existing compounds. Ivermectin belongs to the group of avermectins (AVM), a series of 16-membered macrocyclic lactone compounds discovered in 1967, and FDA-approved for human use in 1987. It has been used by millions of people around the world exhibiting a wide margin of clinical safety. In this review, we summarize the in vitro and in vivo evidences demonstrating that ivermectin exerts antitumor effects in different types of cancer. Ivermectin interacts with several targets including the multidrug resistance protein (MDR), the Akt/mTOR and WNT-TCF pathways, the purinergic receptors, PAK-1 protein, certain cancer-related epigenetic deregulators such as SIN3A and SIN3B, RNA helicase, chloride channel receptors and preferentially target cancer stem-cell like population. Importantly, the in vitro and in vivo antitumor activities of ivermectin are achieved at concentrations that can be clinically reachable based on the human pharmacokinetic studies done in healthy and parasited patients. Thus, existing information on ivermectin could allow its rapid move into clinical trials for cancer patients.

Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey

Computational prediction of drug–target interactions (DTIs) has become an essential task in the drug discovery process. It narrows down the search space for interactions by suggesting potential interaction candidates for validation via wet-lab experiments that are well known to be expensive and time-consuming. In this article, we aim to provide a comprehensive overview and empirical evaluation on the computational DTI prediction techniques, to act as a guide and reference for our fellow researchers. Specifically, we first describe the data used in such computational DTI prediction efforts. We then categorize and elaborate the state-of-the-art methods for predicting DTIs. Next, an empirical comparison is performed to demonstrate the prediction performance of some representative methods under different scenarios. We also present interesting findings from our evaluation study, discussing the advantages and disadvantages of each method. Finally, we highlight potential avenues for further enhancement of DTI prediction performance as well as related research directions.

Mining Filarial Genomes for Diagnostic and Therapeutic Targets

Filarial infections of humans cause some of the most important neglected tropical diseases. The global efforts for eliminating filarial infections by mass drug administration programs may require additional tools (safe macrofilaricidal drugs, vaccines, and diagnostic biomarkers). The accurate and sensitive detection of viable parasites is essential for diagnosis and for surveillance programs. Current community-wide treatment modalities do not kill the adult filarial worms effectively; hence, there is a need to identify and develop safe macrofilaricidal drugs. High-throughput sequencing, mass spectroscopy methods and advances in computational biology have greatly accelerated the discovery process. Here, we describe post-genomic developments toward the identification of diagnostic biomarkers and drug targets for the filarial infection of humans.

Antibiotic-non-antibiotic combinations for combating extremely drug-resistant Gram-negative 'superbugs'

The emergence of antimicrobial resistance of Gram-negative pathogens has become a worldwide crisis. The status quo for combating resistance is to employ synergistic combinations of antibiotics. Faced with this fast-approaching post-antibiotic era, it is critical that we devise strategies to prolong and maximize the clinical efficacy of existing antibiotics. Unfortunately, reports of extremely drug-resistant (XDR) Gram-negative pathogens have become more common. Combining antibiotics such as polymyxin B or the broad-spectrum tetracycline and minocycline with various FDA-approved non-antibiotic drugs have emerged as a novel combination strategy against otherwise untreatable XDR pathogens. This review surveys the available literature on the potential benefits of employing antibiotic-non-antibiotic drug combination therapy. The apex of this review highlights the clinical utility of this novel therapeutic strategy for combating infections caused by 'superbugs'.

Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont

Onchocerciasis (river blindness) is a neglected tropical disease that has been successfully targeted by mass drug treatment programs in the Americas and small parts of Africa. Achieving the long-term goal of elimination of onchocerciasis, however, requires additional tools, including drugs, vaccines, and biomarkers of infection. Here, we describe the transcriptome and proteome profiles of the major vector and the human host stages (L1, L2, L3, molting L3, L4, adult male, and adult female) of Onchocerca volvulus along with the proteome of each parasitic stage and of its Wolbachia endosymbiont (wOv). In so doing, we have identified stage-specific pathways important to the parasite’s adaptation to its human host during its early development. Further, we generated a protein array that, when screened with well-characterized human samples, identified novel diagnostic biomarkers of O. volvulus infection and new potential vaccine candidates. This immunomic approach not only demonstrates the power of this postgenomic discovery platform but also provides additional tools for onchocerciasis control programs.

The global onchocerciasis (river blindness) elimination program will have to rely on the development of new tools (drugs, vaccines, biomarkers) to achieve its goals by 2025. As an adjunct to the completed genomic sequencing of O. volvulus, we used a comprehensive proteomic and transcriptomic profiling strategy to gain a comprehensive understanding of both the vector-derived and human host-derived parasite stages. In so doing, we have identified proteins and pathways that enable novel drug targeting studies and the discovery of novel vaccine candidates, as well as useful biomarkers of active infection.

Gaining Insights Into the Pharmacology of Anthelmintics Using Haemonchus contortus as a Model Nematode

Progress made in understanding pharmacokinetic behaviour and pharmacodynamic mechanisms of drug action/resistance has allowed deep insights into the pharmacology of the main chemical classes, including some of the few recently discovered anthelmintics. The integration of pharmaco-parasitological research approaches has contributed considerably to the optimization of drug activity, which is relevant to preserve existing and novel active compounds for parasite control in livestock. A remarkable amount of pharmacology-based knowledge has been generated using the sheep abomasal nematode Haemonchus contortus as a model. Relevant fundamental information on the relationship among drug influx/efflux balance (accumulation), biotransformation/detoxification and pharmacological effects in parasitic nematodes for the most traditional anthelmintic chemical families has been obtained by exploiting the advantages of working with H. contortus under in vitro, ex vivo and in vivo experimental conditions. The scientific contributions to the pharmacology of anthelmintic drugs based on the use of H. contortus as a model nematode are summarized in the present chapter.

Anthelmintic closantel enhances bacterial killing of polymyxin B against multidrug-resistant Acinetobacter baumannii

Polymyxins, an old class of antibiotics, are currently used as the last resort for the treatment of multidrug-resistant (MDR) Acinetobacter baumannii. However, recent pharmacokinetic and pharmacodynamic data indicate that monotherapy can lead to the development of resistance. Novel approaches are urgently needed to preserve and improve the efficacy of this last-line class of antibiotics. This study examined the antimicrobial activity of novel combination of polymyxin B with anthelmintic closantel against A. baumannii. Closantel monotherapy (16 mg l(-1)) was ineffective against most tested A. baumannii isolates. However, closantel at 4-16 mg l(-1) with a clinically achievable concentration of polymyxin B (2 mg l(-1)) successfully inhibited the development of polymyxin resistance in polymyxin-susceptible isolates, and provided synergistic killing against polymyxin-resistant isolates (MIC ⩾4 mg l(-1)). Our findings suggest that the combination of polymyxin B with closantel could be potentially useful for the treatment of MDR, including polymyxin-resistant, A. baumannii infections. The repositioning of non-antibiotic drugs to treat bacterial infections may significantly expedite discovery of new treatment options for bacterial 'superbugs'.

Onchocerca volvulus Molting Inhibitors Identified through Scaffold Hopping

The anthelmintic closantel has shown promise in abrogating the L3 molting of Onchocerca volvulus, the causative agent of the infectious disease onchocerciasis. In our search for alternative scaffolds, we utilized a fragment replacement/modification approach to generate novel chemotypes with improved chitinase inhibitory properties. Further evaluation of the compounds unveiled the potential of urea-tropolones as potent inhibitors of O. volvulus L3 molting.

A survey of current trends in computational drug repositioning

Computational drug repositioning or repurposing is a promising and efficient tool for discovering new uses from existing drugs and holds the great potential for precision medicine in the age of big data. The explosive growth of large-scale genomic and phenotypic data, as well as data of small molecular compounds with granted regulatory approval, is enabling new developments for computational repositioning. To achieve the shortest path toward new drug indications, advanced data processing and analysis strategies are critical for making sense of these heterogeneous molecular measurements. In this review, we show recent advancements in the critical areas of computational drug repositioning from multiple aspects. First, we summarize available data sources and the corresponding computational repositioning strategies. Second, we characterize the commonly used computational techniques. Third, we discuss validation strategies for repositioning studies, including both computational and experimental methods. Finally, we highlight potential opportunities and use-cases, including a few target areas such as cancers. We conclude with a brief discussion of the remaining challenges in computational drug repositioning.

Exploiting the Polypharmacology of ß-Carbolines to Disrupt O. volvulus Molting

Onchocerciasis is an infection caused by the filarial worm Onchocerca volvulus, which can eventually result in blindness. The lack of an effective macrofilaricide and the possible development of ivermectin-resistant strains of O. volvulus necessitate the need for alternative treatment strategies. We have shown that targeting the L3-stage-specific chitinase OvCHT1 impairs the shedding of the filarial cuticle. In our continued efforts to discover OvCHT1 inhibitors, we identified the β-carboline alkaloid scaffolding as a chitinase inhibitor that is capable of penetrating the worm cuticle. Herein, we disclose the rich polypharmacology of the β-carboline class of compounds as an approach to abrogate the molting of the parasite and thus the initiation of infection in the human host.

Substituted 4-hydroxy-1,2,3-triazoles: synthesis, characterization and first drug design applications through bioisosteric modulation and scaffold hopping approaches

The hydroxytriazole system is here analysed and used to modulate acidic moieties present in lead compounds.

In Vitro Screening for Drug Repositioning

Drug repositioning or repurposing has received much coverage in the scientific literature in recent years and has been responsible for the generation of both new intellectual property and investigational new drug submissions. The literature indicates a significant trend toward the use of computational- or informatics-based methods for generating initial repositioning hypotheses, followed by focused assessment of biological activity in phenotypic assays. Another viable method for drug repositioning is in vitro screening of known drugs or drug-like molecules, initially in disease-relevant phenotypic assays, to identify and validate candidates for repositioning. This approach can use large compound libraries or can focus on subsets of known drugs or drug-like molecules. In this short review, we focus on ways to generate and validate repositioning candidates in disease-related in vitro and phenotypic assays, and we discuss specific examples of this approach as applied to a variety of disease areas. We propose that in vitro screens offer several advantages over biochemical or in vivo methods as a starting point for drug repositioning.

Chemotherapy in the treatment, control, and elimination of human onchocerciasis

Onchocerciasis treatment is one of the most positive stories in tropical medicine although major challenges remain to reaching the ultimate goal of disease elimination. Such challenges are to be expected when the therapeutic goal is to kill and safely remove a large multistage, efficient, metazoan infectious agent such as Onchocerca volvulus that has an exceptionally complicated relationship with its host. Successful control of onchocerciasis has often been hampered by host reactions following chemotherapy, that can sometimes cause significant tissue pathology. Presence of other filariae, particularly Loa loa, in endemic onchocerciasis-treatment areas also poses severe problems due to adverse reactions caused by drug-induced death of the coincident microfilariae of this usually clinically benign species. Although ivermectin has been very successful, there is a need to enhance the progress toward elimination of onchocerciasis; new drugs and their efficient use are keys to this. The permanent absence of Onchocerca microfilaridermia, defined as the lack of resurgence of skin microfilarial loads after treatment, is the ultimate characteristic of a useful new chemotherapeutic agent. Several drugs are under investigation to achieve this, including the reassessment of currently available and previously tested agents, such as the antibiotic, doxycycline, which targets the adult parasites through its anti-Wolbachia endosymbiont activity. Flubendazole, a benzimidazole derivative approved for treatment of human gastrointestinal nematodes, is also being considered for repurposing as a macrofilaricide to aid in the achievement of eradication. The managerial challenges existing at the population level also need to be addressed; these include drug-distribution fatigue, the need to include noncompliant people, civil unrest in endemic areas, political cross-border issues, restrictions of age and pregnancy, and complications due to integration with other treatment programs. It is likely that a panel of chemotherapeutic options, new and old, supported by strong and effective distribution systems will be the best way to address challenges of treatment and elimination of this infection. Future research should also address management of treatment and control, and consider how new treatment paradigms can be incorporated to meet time lines set for global elimination by 2025.

The Impact of Nurses on Neglected Tropical Disease Management

Although Neglected Tropical Diseases (NTDs) are largely endemic in the developing nations of Africa, Asia, and South and Central America, they are reemerging with increasing frequency in developed countries. Their diagnosis, treatment, and control are an increasing public health concern that requires a different awareness by health care providers. Neglected tropical diseases (NTDs) are chronic infectious diseases which disproportionately burden poor, rural, and marginalized populations with significant mortality and high morbidity (disability, disfigurement, impaired childhood growth and cognitive development, increased vulnerability to coinfection) that reinforces their poverty. What can we learn from the nurses in developing countries already battling NTD's that could be useful in the developed world? This article provides an overview of distribution, pathophysiology, symptoms, and management of 13 NTDs, with particular attention to the role of nurses in delivering cost-effective integrated interventions. Case studies of schistosomiasis, Chagas disease, and leishmaniasis address recognition and treatment of infected individuals in developed nations where NTD infection is limited primarily to immigrants and travelers.

A target repurposing approach identifies N-myristoyltransferase as a new candidate drug target in filarial nematodes

Myristoylation is a lipid modification involving the addition of a 14-carbon unsaturated fatty acid, myristic acid, to the N-terminal glycine of a subset of proteins, a modification that promotes their binding to cell membranes for varied biological functions. The process is catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT), an enzyme which has been validated as a drug target in human cancers, and for infectious diseases caused by fungi, viruses and protozoan parasites. We purified Caenorhabditis elegans and Brugia malayi NMTs as active recombinant proteins and carried out kinetic analyses with their essential fatty acid donor, myristoyl-CoA and peptide substrates. Biochemical and structural analyses both revealed that the nematode enzymes are canonical NMTs, sharing a high degree of conservation with protozoan NMT enzymes. Inhibitory compounds that target NMT in protozoan species inhibited the nematode NMTs with IC₅₀ values of 2.5–10 nM, and were active against B. malayi microfilariae and adult worms at 12.5 µM and 50 µM respectively, and C. elegans (25 µM) in culture. RNA interference and gene deletion in C. elegans further showed that NMT is essential for nematode viability. The effects observed are likely due to disruption of the function of several downstream target proteins. Potential substrates of NMT in B. malayi are predicted using bioinformatic analysis. Our genetic and chemical studies highlight the importance of myristoylation in the synthesis of functional proteins in nematodes and have shown for the first time that NMT is required for viability in parasitic nematodes. These results suggest that targeting NMT could be a valid approach for the development of chemotherapeutic agents against nematode diseases including filariasis.

Lymphatic filariasis and onchocerciasis are neglected tropical diseases caused by filarial nematodes. The limitations of existing drugs to treat these infections highlight the need for new drugs. In the present study, we investigated myristoylation, a lipid modification of a subset of proteins that promotes their binding to cell membranes for varied biological functions. The process is catalyzed by N-myristoyltransferase (NMT), an enzyme which has been validated as a drug target in protozoan parasites. We performed kinetic analyses on Caenorhabditis elegans and Brugia malayi NMTs. NMT inhibitors were active against B. malayi microfilariae and adult worms, and C. elegans in culture. RNA interference and gene deletion in C. elegans further demonstrated that NMT is essential for nematode viability. Our genetic and chemical studies indicate the importance of myristoylation in the synthesis of functional proteins in nematodes and have shown for the first time that NMT is required for viability in parasitic nematodes. These results suggest that targeting NMT could be a valid approach for the development of new therapies against nematode infection including filarial diseases.

Dual protonophore-chitinase inhibitors dramatically affect O. volvulus molting

The L3-stage-specific chitinase OvCHT1 has been implicated in the development of Onchocerca volvulus, the causative agent of onchocerciasis. Closantel, a known anthelmintic drug, was previously discovered as a potent and specific OvCHT1 inhibitor. As closantel is also a known protonophore, we performed a simple scaffold modulation to map out the structural features that are relevant for its individual or dual biochemical roles. Furthermore, we present that either OvCHT1 inhibition or protonophoric activity was capable of affecting O. volvulus L3 molting and that the presence of both activities in a single molecule yielded more potent inhibition of the nematode’s developmental process.

Repositioning: the fast track to new anti-malarial medicines?

BACKGROUND

Repositioning of existing drugs has been suggested as a fast track for developing new anti-malarial agents. The compound libraries of GlaxoSmithKline (GSK), Pfizer and AstraZeneca (AZ) comprising drugs that have undergone clinical studies in other therapeutic areas, but not achieved approval, and a set of US Food and Drug Administration (FDA)-approved drugs and other bio-actives were tested against Plasmodium falciparum blood stages.

METHODS

Molecules were tested initially against erythrocytic co-cultures of P. falciparum to measure proliferation inhibition using one of the following methods: SYBR®I dye DNA staining assay (3D7, K1 or NF54 strains); [(3)H] hypoxanthine radioisotope incorporation assay (3D7 and 3D7A strain); or 4',6-diamidino-2-phenylindole (DAPI) DNA imaging assay (3D7 and Dd2 strains). After review of the available clinical pharmacokinetic and safety data, selected compounds with low μM activity and a suitable clinical profile were tested in vivo either in a Plasmodium berghei four-day test or in the P. falciparum Pf3D7(0087/N9) huSCID 'humanized' mouse model.

RESULTS

Of the compounds included in the GSK and Pfizer sets, 3.8% (9/238) had relevant in vitro anti-malarial activity while 6/100 compounds from the AZ candidate drug library were active. In comparison, around 0.6% (24/3,800) of the FDA-approved drugs and other bio-actives were active. After evaluation of available clinical data, four investigational drugs, active in vitro were tested in the P. falciparum humanized mouse model: UK-112,214 (PAF-H1 inhibitor), CEP-701 (protein kinase inhibitor), CEP-1347 (protein kinase inhibitor), and PSC-833 (p-glycoprotein inhibitor). Only UK-112,214 showed significant efficacy against P. falciparum in vivo, although at high doses (ED90 131.3 mg/kg [95% CI 112.3, 156.7]), and parasitaemia was still present 96 hours after treatment commencement. Of the six actives from the AZ library, two compounds (AZ-1 and AZ-3) were marginally efficacious in vivo in a P. berghei model.

CONCLUSIONS

Repositioning of existing therapeutics in malaria is an attractive proposal. Compounds active in vitro at μM concentrations were identified. However, therapeutic concentrations may not be effectively achieved in mice or humans because of poor bio-availability and/or safety concerns. Stringent safety requirements for anti-malarial drugs, given their widespread use in children, make this a challenging area in which to reposition therapy.

Whole animal automated platform for drug discovery against multi-drug resistant Staphylococcus aureus

Staphylococcus aureus, the leading cause of hospital-acquired infections in the United States, is also pathogenic to the model nematode Caenorhabditis elegans. The C. elegans-S. aureus infection model was previously carried out on solid agar plates where the bacteriovorous C. elegans feeds on a lawn of S. aureus. However, agar-based assays are not amenable to large scale screens for antibacterial compounds. We have developed a high throughput liquid screening assay that uses robotic instrumentation to dispense a precise amount of methicillin resistant S. aureus (MRSA) and worms in 384-well assay plates, followed by automated microscopy and image analysis. In validation of the liquid assay, an MRSA cell wall defective mutant, MW2ΔtarO, which is attenuated for killing in the agar-based assay, was found to be less virulent in the liquid assay. This robust assay with a Z'-factor consistently greater than 0.5 was utilized to screen the Biomol 4 compound library consisting of 640 small molecules with well characterized bioactivities. As proof of principle, 27 of the 30 clinically used antibiotics present in the library conferred increased C. elegans survival and were identified as hits in the screen. Surprisingly, the antihelminthic drug closantel was also identified as a hit in the screen. In further studies, we confirmed the anti-staphylococcal activity of closantel against vancomycin-resistant S. aureus isolates and other Gram-positive bacteria. The liquid C. elegans-S. aureus assay described here allows screening for anti-staphylococcal compounds that are not toxic to the host.

Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor

The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation.