PPLK+C: A Bioinformatics Tool for Predicting Peptide Ligands of Potassium Channels Based on Primary Structure Information

NaII-Pred: An ensemble-learning framework for the identification and interpretation of sodium ion inhibitors by fusing multiple feature representation

High-affinity ligand peptides for ion channels are essential for controlling the flow of ions across the plasma membrane. These peptides are now being investigated as possible therapeutic possibilities for a variety of illnesses, including cancer and cardiovascular disease. So, the identification and interpretation of ligand peptide inhibitors to control ion flow across cells become pivotal for exploration. In this work, we developed an ensemble-based model, NaII-Pred, for the identification of sodium ion inhibitors. The ensemble model was trained, tested, and evaluated on three different datasets. The NaII-Pred method employs six different descriptors and a hybrid feature set in conjunction with five conventional machine learning classifiers to create 35 baseline models. Through an ensemble approach, the top five baseline models trained on the hybrid feature set were integrated to yield the final predictive model, NaII-Pred. Our proposed model, NaII-Pred, outperforms the baseline models and the current predictors on both datasets. We believe NaII-Pred will play a critical role in screening and identifying potential sodium ion inhibitors and will be an invaluable tool.

Leveraging a meta-learning approach to advance the accuracy of Nav blocking peptides prediction

The voltage-gated sodium (Nav) channel is a crucial molecular component responsible for initiating and propagating action potentials. While the α subunit, forming the channel pore, plays a central role in this function, the complete physiological function of Nav channels relies on crucial interactions between the α subunit and auxiliary proteins, known as protein-protein interactions (PPI). Nav blocking peptides (NaBPs) have been recognized as a promising and alternative therapeutic agent for pain and itch. Although traditional experimental methods can precisely determine the effect and activity of NaBPs, they remain time-consuming and costly. Hence, machine learning (ML)-based methods that are capable of accurately contributing in silico prediction of NaBPs are highly desirable. In this study, we develop an innovative meta-learning-based NaBP prediction method (MetaNaBP). MetaNaBP generates new feature representations by employing a wide range of sequence-based feature descriptors that cover multiple perspectives, in combination with powerful ML algorithms. Then, these feature representations were optimized to identify informative features using a two-step feature selection method. Finally, the selected informative features were applied to develop the final meta-predictor. To the best of our knowledge, MetaNaBP is the first meta-predictor for NaBP prediction. Experimental results demonstrated that MetaNaBP achieved an accuracy of 0.948 and a Matthews correlation coefficient of 0.898 over the independent test dataset, which were 5.79% and 11.76% higher than the existing method. In addition, the discriminative power of our feature representations surpassed that of conventional feature descriptors over both the training and independent test datasets. We anticipate that MetaNaBP will be exploited for the large-scale prediction and analysis of NaBPs to narrow down the potential NaBPs.

Nanomedicine based potentially transformative strategies for colon targeting of peptides: State-of-the-art

Recently, peptides have attracted tremendous attention among researchers attributed to their high target specificity and efficacy compared to conventional therapeutics. The ease of self-administration and non-invasiveness confers oral as the most desirable route. However, numerous challenges associated with peptide delivery through the oral route like harsh gastrointestinal environment, enzymatic degradation, and absorption barriers hinder its clinical translation. Protease activity is more pronounced in the proximal segments of the gastrointestinal tract (GIT). Distal segments like the colon possess lower proteolytic activity, enhanced retention time, etc. which could facilitate easy absorption. However, traversing of the upper segments to reach the colon requires the circumvention of the pitfalls of the GIT. The advent of nanomedicine strategies could help in overcoming the said challenges associated with oral delivery, colon-specific targeting, and improving stability and bioavailability at the active site. Furthermore, the classification of peptides and various nanomedicine strategies for oral delivery of peptides to the colon has been conveyed. Regulatory hurdles and ways to accomplish clinical translation have been addressed.

Multi-Branch-CNN: Classification of ion channel interacting peptides using multi-branch convolutional neural network

Ligand peptides that have high affinity for ion channels are critical for regulating ion flux across the plasma membrane. These peptides are now being considered as potential drug candidates for many diseases, such as cardiovascular disease and cancers. In this work, we developed Multi-Branch-CNN, a CNN method with multiple input branches for identifying three types of ion channel peptide binders (sodium, potassium, and calcium) from intra- and inter-feature types. As for its real-world applications, prediction models that are able to recognize novel sequences having high or low similarities to training sequences are required. To this end, we tested our models on two test sets: a general test set including sequences spanning different similarity levels to those of the training set, and a novel-test set consisting of only sequences that bear little resemblance to sequences from the training set. Our experiments showed that the Multi-Branch-CNN method performs better than thirteen traditional ML algorithms (TML13), yielding an improvement in accuracy of 3.2%, 1.2%, and 2.3% on the test sets as well as 8.8%, 14.3%, and 14.6% on the novel-test sets for sodium, potassium, and calcium ion channels, respectively. We confirmed the effectiveness of Multi-Branch-CNN by comparing it to the standard CNN method with one input branch (Single-Branch-CNN) and an ensemble method (TML13-Stack). The data sets, script files to reproduce the experiments, and the final predictive models are freely available at https://github.com/jieluyan/Multi-Branch-CNN.

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions

The interactions between miRNAs and long non-coding RNAs (lncRNAs) are subject to intensive recent studies due to its critical role in gene regulations. Computational prediction of lncRNA-miRNA interactions has become a popular alternative strategy to the experimental methods for identification of underlying interactions. It is desirable to develop the machine learning-based models for prediction of lncRNA-miRNA based on the experimentally validated interactions between lncRNAs and miRNAs. The accuracy and robustness of existing models based on machine learning techniques are subject to further improvement. Considering that the attributes of lncRNA and miRNA contribute key importance in the interaction between these two RNAs, a deep learning model, named LMI-DForest, is proposed here by combining the deep forest and autoencoder strategies. Systematic comparison on the experiment validated datasets for lncRNA-miRNA interaction datasets demonstrates that the proposed method consistently shows superior performance over the other machine learning models in the lncRNA-miRNA interaction prediction.