Efficacy and safety of next-generation tick transcriptome-derived direct thrombin inhibitors

Prospection of Peptide Inhibitors of Thrombin from Diverse Origins Using a Machine Learning Pipeline

Thrombin is a key enzyme involved in the development and progression of many cardiovascular diseases. Direct thrombin inhibitors (DTIs), with their minimum off-target effects and immediacy of action, have greatly improved the treatment of these diseases. However, the risk of bleeding, pharmacokinetic issues, and thrombotic complications remain major concerns. In an effort to increase the effectiveness of the DTI discovery pipeline, we developed a two-stage machine learning pipeline to identify and rank peptide sequences based on their effective thrombin inhibitory potential. The positive dataset for our model consisted of thrombin inhibitor peptides and their binding affinities (KI) curated from published literature, and the negative dataset consisted of peptides with no known thrombin inhibitory or related activity. The first stage of the model identified thrombin inhibitory sequences with Matthew's Correlation Coefficient (MCC) of 83.6%. The second stage of the model, which covers an eight-order of magnitude range in KI values, predicted the binding affinity of new sequences with a log room mean square error (RMSE) of 1.114. These models also revealed physicochemical and structural characteristics that are hidden but unique to thrombin inhibitor peptides. Using the model, we classified more than 10 million peptides from diverse sources and identified unique short peptide sequences (<15 aa) of interest, based on their predicted KI. Based on the binding energies of the interaction of the peptide with thrombin, we identified a promising set of putative DTI candidates. The prediction pipeline is available on a web server.

The diurnal salivary glands transcriptome of Dermacentor nuttalli from the first four days of blood feeding

The ixodid tick Dermacentor nuttalli is distributed from southern Siberia to North China and is a vector of many pathogens. This species can have severe impacts on animal husbandry and human health. To date, the control of D. nuttalli is limited to the use of acaricides such as organophosphorus, synthetic pyrethroids and amidine pesticides. There are no environmentally friendly or reliable prevention and control measures, and little is known regarding key antigens involved in blood feeding. Salivary glands are major tissues involved in the blood feeding and pathogen transmission of ticks. Therefore, this study focused on salivary glands tissue to identify the dominant antigens of D. nuttalli involved in tick feeding. For this, high-throughput RNA sequencing (RNA-seq) was used for analysis. The transcriptome of female D. nuttalli ticks was assembled and characterized, and differentially expressed genes (DEGs) were identified in the salivary glands of ticks that had not fed (0 h) and of ticks after 24, 48, 72 and 96 h of feeding. There were 22,802,784, 22,275,013, 26,629,453, 24,982,389, and 22,596,230 high-quality clean reads obtained from salivary glands tissues at the five different blood feeding time points. The total number of annotated unigenes was 100,347. The differences in gene expression between different time points were compared, and functional enrichment was performed. Quantitative reverse transcription PCR (RT‒qPCR) was used to validate the RNA-seq results, the results of which showed that the differences in expressed transcripts presented similar trends. Among the identified DEGs, the most numerous were those with catalytic and binding activities and those involved in diverse metabolic pathways and cellular processes. The expression patterns of homologous and family-member proteins throughout the blood feeding period exhibited significant differences, strongly suggesting that the transcriptome composition is highly dynamic and likely subjected to important variation throughout the life cycle. Studies of gene sequences in D. nuttalli will greatly increase the information on tick protective antigens, which could potentially function as effective vaccine candidates or drug targets for the development of environmentally friendly acaricides.

Purification and characterization of thrombin from camel plasma: interaction with camel tick salivary gland thrombin inhibitor

BACKGROUND

Thrombin is the most important enzyme in the hemostatic process by permitting rapid and localized coagulation in case of tissue damage. Camel thrombin is the natural and proper target enzyme for the previously purified camel tick salivary gland thrombin inhibitor.

RESULTS

In this study, the camel thrombin was purified homogenously in a single affinity chromatographic step on the heparin-agarose affinity column with a specific activity of 3242 NIH units/mg proteins. On SDS-PAGE, the purified camel thrombin contained two forms, 37 kDa α-thrombin and 28 kDa β-thrombin, and the camel prothrombin was visualized as 72 kDa. The camel thrombin Km value was found out as 60 µM of N-(p-Tosyl)-Gly-Pro-Arg-p-nitroanilide acetate and displayed its optimum activity at pH 8.3. The PMSF was the most potent inhibitor of camel thrombin. Camel tick salivary gland thrombin inhibitor has two binding sites on camel thrombin and inhibited it competitively with Ki value of 0.45 µM.

CONCLUSIONS

The purified camel thrombin was found to be more susceptible toward the camel tick salivary gland thrombin inhibitor than bovine thrombin.

Improving treatment for acute ischemic stroke—Clot busting innovation in the pipeline

Acute ischemic stroke is a consequence of disrupted blood flow to the brain, caused by thrombosis—the pathological formation of occlusive clots within blood vessels, which can embolize distally to downstream tissues and microvasculature. The highest priority of stroke treatment is the rapid removal of occlusive clots and restoration of tissue perfusion. Intravenous thrombolysis is the pharmacological standard-of-care for the dissolution of blood clots, wherein thrombolytic drugs are administered to restore vessel patency. While the introduction of recombinant tissue-plasminogen activator (rtPA) in 1996 demonstrated the benefit of acute thrombolysis for clot removal, this was countered by severe limitations in terms of patient eligibility, lytic efficacy, rethrombosis and safety implications. Development of safer and efficacious treatment strategies to improve clot lysis has not significantly progressed over many decades, due to the challenge of maintaining the necessary efficacy-safety balance for these therapies. As such, rtPA has remained the sole approved acute therapeutic for ischemic stroke for over 25 years. Attempts to improve thrombolysis with coadministration of adjunct antithrombotics has demonstrated benefit in coronary vessels, but remain contraindicated for stroke, given all currently approved antithrombotics adversely impact hemostasis, causing bleeding. This Perspective provides a brief history of stroke drug development, as well as an overview of several groups of emerging drugs which have the potential to improve thrombolytic strategies in the future. These include inhibitors of the platelet receptor glycoprotein VI and the signaling enzyme PI3-Kinase, novel anticoagulants derived from hematophagous creatures, and proteolysis-targeting chimeras.