Discovery of anticancer peptides from natural and generated sequences using deep learning.

Anticancer peptides (ACPs) demonstrate significant potential in clinical cancer treatment due to their ability to selectively target and kill cancer cells. In recent years, numerous artificial intelligence (AI) algorithms have been developed. However, many predictive methods lack sufficient wet lab validation, thereby constraining the progress of models and impeding the discovery of novel ACPs.

Multi-omics profiling combined with molecular docking reveals immune-inflammatory proteins as potential drug targets in colorectal cancer.

Colorectal cancer is globally ranked as the third most common malignant tumor. Its development involves a complex biological process driven by various genetic and epigenetic alterations. To elucidate the biological significance of the extensive omics data, we conducted comparative multi-omics studies on colorectal cancer patients at different clinical stages.

Discovery of potential antidiabetic peptides using deep learning.

Antidiabetic peptides (ADPs), peptides with potential antidiabetic activity, hold significant importance in the treatment and control of diabetes. Despite their therapeutic potential, the discovery and prediction of ADPs remain challenging due to limited data, the complex nature of peptide functions, and the expensive and time-consuming nature of traditional wet lab experiments. This study aims to address these challenges by exploring methods for the discovery and prediction of ADPs using advanced deep learning techniques.

Discovery of the Inhibitor Targeting the SLC7A11/xCT Axis through In Silico and In Vitro Experiments.

In the development and progression of cervical cancer, oxidative stress plays an important role within the cells. Among them, Solute Carrier Family 7 Member 11 (SLC7A11/xCT) is crucial for maintaining the synthesis of glutathione and the antioxidant system in cervical cancer cells. In various tumor cells, studies have shown that SLC7A11 inhibits ferroptosis, a form of cell death, by mediating cystine uptake and maintaining glutathione synthesis.

Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay.

Lactate dehydrogenase A (LDHA) is highly expressed in many tumor cells and promotes the conversion of pyruvate to lactic acid in the glucose pathway, providing energy and synthetic precursors for rapid proliferation of tumor cells. Therefore, inhibition of LDHA has become a widely concerned tumor treatment strategy. However, the research and development of highly efficient and low toxic LDHA small molecule inhibitors still faces challenges.

ToxMPNN: A deep learning model for small molecule toxicity prediction.

Machine learning (ML) has shown a great promise in predicting toxicity of small molecules. However, the availability of data for such predictions is often limited. Because of the unsatisfactory performance of models trained on a single toxicity endpoint, we collected toxic small molecules with multiple toxicity endpoints from previous study.

Targeting the PDK/PDH axis to reverse metabolic abnormalities by structure-based virtual screening with in vitro and in vivo experiments.

In humans and animals, the pyruvate dehydrogenase kinase (PDK) family proteins (PDKs 1-4) are excessively activated in metabolic disorders such as obesity, diabetes, and cancer, inhibiting the activity of pyruvate dehydrogenase (PDH) which plays a crucial role in energy and fatty acid metabolism and impairing its function. Intervention and regulation of PDH activity have become important research approaches for the treatment of various metabolic disorders. In this study, a small molecule (g25) targeting PDKs and activating PDH, was identified through multi-level computational screening methods.

Molecular action mechanisms of two novel and selective calcium release-activated calcium channel antagonists.

The prototypical calcium release-activated calcium (CRAC) channel, composed of STIM1 and Orai1, is a sought-after drug target for treating autoimmune disorders. Herein, we identified two novel and selective CRAC channel inhibitors, the indole-like compound C63368 and pyrazole core-containing compound C79413, potently and reversibly inhibiting the CRAC channel with low micromolar ICs and sparing various off-target ion channels. These two compounds did not inhibit STIM1 activation or its coupling with Orai1, nor did they affect the channel's calcium-dependent fast inactivation.

Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.

Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids.

Dual-sensitive antibacterial peptide nanoparticles prevent dental caries.

Dental caries is the most prevalent bacterial biofilm-induced disease. Current clinical prevention and treatment agents often suffer from adverse effects on oral microbiota diversity and normal tissues, predominately arising from the poor biofilm-targeting property of the agents. To address this concern, we herein report dual-sensitive antibacterial peptide nanoparticles pHly-1 NPs upon acid and lipid-binding for treatment of dental caries.

The small molecule compound C65780 alleviates pain by stabilizing voltage-gated sodium channels in the inactivated and slowly-recovering state.

Noxious pain signals are transduced in the peripheral nervous system as action potentials, which rely on the activities of voltage-gated sodium channels (NaVs). Blocking NaVs is thus a valuable strategy for pain treatment. Here, we report the characterization of a novel NaVs antagonist, 2-(2-(diethylamino)ethyl)indeno[1,2,3-de]phthalazin-3(2H)-one (C65780), and investigation of its action mechanisms.

Characterization of a novel affinity binding ligand for tyrosine nitrated peptides from a phage-displayed peptide library.

As an important post-translational modification in response to oxidative and nitrosative stress, protein tyrosine nitration is deeply involved in many physiological and pathological processes. Identifying tyrosine nitration in proteins is challenging due to its low abundance.Consequently, pre-separation and enrichment of tyrosine-nitrated peptides (TNPs) are necessary before submitting them to mass spectrometry analysis.

A Novel Spider Toxin Inhibits Fast Inactivation of the Na1.9 Channel by Binding to Domain III and Domain IV Voltage Sensors.

Venomous animals have evolved to produce peptide toxins that modulate the activity of voltage-gated sodium (Na) channels. These specific modulators are powerful probes for investigating the structural and functional features of Na channels. Here, we report the isolation and characterization of δ-theraphotoxin-Gr4b (Gr4b), a novel peptide toxin from the venom of the spider Gr4b contains 37-amino acid residues with six cysteines forming three disulfide bonds Patch-clamp analysis confirmed that Gr4b markedly slows the fast inactivation of Na1.

Molecular mechanisms of centipede toxin SsTx-4 inhibition of inwardly rectifying potassium channels.

Inwardly rectifying potassium channels (Kirs) are important drug targets, with antagonists for the Kir1.1, Kir4.1, and pancreatic Kir6.

Glucose-Lipopeptide Conjugates Reveal the Role of Glucose Modification Position in Complexation and the Potential of Malignant Melanoma Therapy.

Glycosylation and fatty acid modification are promising strategies to improve peptide performance. We previously studied glycosylation and fatty acid modification of the anticancer peptide R-lycosin-I. In this study, we further investigated the co-modification of fatty acids and monosaccharides in R-lycosin-I.

Variation of Two S3b Residues in K4.1-4.3 Channels Underlies Their Different Modulations by Spider Toxin κ-LhTx-1.

The naturally occurred peptide toxins from animal venoms are valuable pharmacological tools in exploring the structure-function relationships of ion channels. Herein we have identified the peptide toxin κ-LhTx-1 from the venom of spider (the Lichen huntsman spider) as a novel selective antagonist of the K4 family potassium channels. κ-LhTx-1 is a gating-modifier toxin impeded K4 channels' voltage sensor activation, and mutation analysis has confirmed its binding site on channels' S3b region.

Engineering of highly potent and selective HNTX-III mutant against hNa1.7 sodium channel for treatment of pain.

Human voltage-gated sodium channel Na1.7 (hNa1.7) is involved in the generation and conduction of neuropathic and nociceptive pain signals.

Molecular diversification of antimicrobial peptides from the wolf spider Lycosa sinensis venom based on peptidomic, transcriptomic, and bioinformatic analyses.

The venom of Lycosoidea spiders is a complex multicomponent mixture of neurotoxic peptides (main components) and antimicrobial peptides (AMPs) as minor components. In this study, we described the high-throughput identification and analysis of AMPs from Lycosa sinensis venom (named LS-AMPs) using a combination strategy that includes the following three different analysis approaches: (i) peptidomic analysis, namely reversed-phase high-performance liquid chromatography (RP-HPLC) separation plus top-down sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS); (ii) transcriptomic analysis, namely cDNA library construction plus DNA sequencing; (iii) bioinformatic analysis, namely analysis and prediction for molecular characters of LS-AMPs by the online biology databases. In total, 52 sequences of AMPs were identified from L.

Drug-Bearing Peptide-Based Nanospheres for the Inhibition of Metastasis and Growth of Cancer.

Employing a peptide-based nanoscale drug delivery system is an effective strategy to overcome the poor therapeutic outcomes of chemotherapeutic drugs. Here, we developed a self-assembling peptide-drug delivery system comprising a self-assembling anticancer peptide (R-lycosin-I), as revealed in our previous study, and 10-hydroxycamptothecin (HCPT) for cancer therapy. The results showed that peptide-drug conjugates (R-L-HCPT) could assemble into nanospheres of 40-60 nm in water.

Jingzhaotoxin-X, a gating modifier of Kv4.2 and Kv4.3 potassium channels purified from the venom of the Chinese tarantula .

Background: The tarantula is one of the largest venomous spiders in China. In previous studies, we purified and characterized at least eight peptides from venom. In this report, we describe the purification and characterization of Jingzhaotoxin-X (JZTX-X), which selectively blocks Kv4.

Spider venom-derived peptide induces hyperalgesia in Na1.7 knockout mice by activating Na1.9 channels.

The sodium channels Na1.7, Na1.8 and Na1.

Scorpion toxin inhibits the voltage-gated proton channel using a Zn -like long-range conformational coupling mechanism.

Background And Purpose: Blocking the voltage-gated proton channel H 1 is a promising strategy for the treatment of diseases like ischaemia stroke and cancer. However, few H 1 channel antagonists have been reported. Here, we have identified a novel H 1 channel antagonist from scorpion venom and have elucidated its action mechanism.