Generation of functional oligopeptides that promote osteogenesis based on unsupervised deep learning of protein IDRs

NuanXin Formula inhibits bone resorption to combat osteoporosis by attenuating osteoclast oxidative phosphorylation

ETHNOPHARMACOLOGICAL RELEVANCE

Osteoporosis is a chronic metabolic bone disorder characterized by excessive bone resorption. The NuanXin Formula (NX) is a classical traditional Chinese medicine formula that can warm and tonify kidney Yang, as well as replenish Qi and blood, which are essential for maintaining bone health and regulating bone metabolism. Nevertheless, the functions and mechanisms of NX in osteoporosis therapy remain unclear.

AIM OF THE STUDY

This study aims to evaluate the effects and mechanisms of NX on osteoclastogenesis and to investigate its potential in combating osteoporosis.

MATERIALS AND METHODS

The inhibitory effects of NX on RANKL-induced osteoclastogenesis were evaluated using Western blotting, quantitative PCR (Q-PCR), TRAP staining, and pit-formation assays. Bone mass and structure were assessed through micro-CT, biomechanical testing, TRAP staining, IHC staining, and H&E staining. The mechanism of action of NX on osteoclasts was investigated using RNA sequencing, ROS staining, ATP measurement, and mitochondrial membrane potential assays.

RESULTS

The in vitro findings demonstrated that NX treatment significantly inhibited osteoclast differentiation and bone resorption activity. Q-PCR and WB analyses indicated that NX substantially downregulates the expression levels of key osteoclast markers, including Nfatc1, Ctsk, Mmp9, and Trap. In vivo experiments revealed that intragastric administration of NX effectively suppressed bone loss and bone resorption, while enhancing the biomechanical properties of bone in ovariectomized (OVX) mice. Mechanistically, NX inhibits oxidative phosphorylation (OXPHOS), decreases mitochondrial membrane potential, and reduces ATP production and reactive oxygen species generation, thereby impeding osteoclast differentiation and activity.

CONCLUSION

NX mitigates osteoporosis by modulating OXPHOS to inhibit osteoclast differentiation and activity, thus offering a potential therapeutic approach for osteoporosis management. However, the study has limitations that require further investigation. NX did not show a clear dose-dependent effect in animal tests, suggesting a need for improved dosing designs. Although we emphasize NX's therapeutic potential, more research is necessary to clarify its mechanism. Variability in plant materials and ingredient ratios might influence NX's pharmacological effects, with specific bioactive components potentially playing a major role. Future research should integrate network pharmacology with experimental validation for a more thorough understanding.

Throw out an oligopeptide to catch a protein: Deep learning and natural language processing-screened tripeptide PSP promotes Osteolectin-mediated vascularized bone regeneration

Angiogenesis is imperative for bone regeneration, yet the conventional cytokine therapies have been constrained by prohibitive costs and safety apprehensions. It is urgent to develop a safer and more efficient therapeutic alternative. Herein, utilizing the methodologies of Deep Learning (DL) and Natural Language Processing (NLP), we proposed a paradigm algorithm that amalgamates Word2vec with a TF-IDF variant, TF-IIDF, to deftly discern potential pro-angiogenic peptides from intrinsically disordered regions (IDRs) of 262 related proteins, where are fertile grounds for developing safer and highly promising bioactive peptides. After the evaluation of the candidate oligopeptides, one tripeptide, PSP, emerged as particularly notable for its exceptional ability to stimulate the vascularization of endothelial cells (ECs), enhance vascular-osteo communication, and then boost the osteogenic differentiation of bone marrow stem cells (BMSCs), evidenced in mouse critical-sized cranial model. Moreover, we found that PSP serves as a 'priming' agent, activating the body's innate ability to produce Osteolectin (Oln) - prompting ECs to release small extracellular vesicles (sEVs) enriched with Oln to facilitate bone formation. In summary, our study established a precise and efficient composite model of DL and NLP to screen bioactive peptides, opening an avenue for the development of various peptide-based therapeutic strategies applicable to a broader range of diseases.

Effect of chitosan on buck semen quality and semen plasma metabolites during low-temperature storage

Background

Optimizing buck semen preservation techniques can significantly advance the goat industry. This study aimed to investigate the effects of chitosan on sperm quality and seminal plasma metabolite profiles in bucks during low-temperature storage at 4°C.

Results

The results showed that when 0.2 mg/mL chitosan was added to semen dilution, sperm viability and antioxidant capacity were highest and significantly higher than the control group (p < 0.05). Sperm viability decreased progressively with increasing storage time at 4°C. However, on day 5, sperm viability was significantly higher in all groups where chitosan was added to the semen dilutions than in the control group (p < 0.05). A total of 23 classes of metabolites were detected in the non-targeted metabolism group of seminal plasma. The metabolite caused by chitosan mainly included fatty acyls, phospholipids, amino acids and organic acids. Most differential metabolites in fatty acyls and glycerophospholipids in chitosan-treated semen were decreased and enriched in the anabolic pathway of unsaturated fatty acids. Additionally, several oligopeptides showed correlations with sperm quality.

Conclusion

These results suggest that adding 0.2 mg/mL chitosan to semen diluent successfully prolongs the low-temperature preservation of semen mainly by altering the anabolism of lipids and amino acids. This provides theoretical support and practical reference for the applying chitosan in the low-temperature preservation of buck semen.

Large Model Era: Deep Learning in Osteoporosis Drug Discovery

Osteoporosis is a systemic microstructural degradation of bone tissue, often accompanied by fractures, pain, and other complications, resulting in a decline in patients' life quality. In response to the increased incidence of osteoporosis, related drug discovery has attracted more and more attention, but it is often faced with challenges due to long development cycle and high cost. Deep learning with powerful data processing capabilities has shown significant advantages in the field of drug discovery. With the development of technology, it is more and more applied to all stages of drug discovery. In particular, large models, which have been developed rapidly recently, provide new methods for understanding disease mechanisms and promoting drug discovery because of their large parameters and ability to deal with complex tasks. This review introduces the traditional models and large models in the deep learning domain, systematically summarizes their applications in each stage of drug discovery, and analyzes their application prospect in osteoporosis drug discovery. Finally, the advantages and limitations of large models are discussed in depth, in order to help future drug discovery.

Analytical and drug delivery strategies for short peptides: From manufacturing to market

In recent times, biopharmaceuticals have gained attention because of their tremendous potential to benefit millions of patients globally by treating widespread diseases such as cancer, diabetes and many rare diseases. Short peptides (SP), also termed as oligopeptides, are one such class of biopharmaceuticals, that are majorly involved in efficient functioning of biological systems. Peptide chains that are 2-20 amino acids long are considered as oligopeptides by researchers and are some of the functionally vital compounds with widespread applications including self-assembly material for drug delivery, targeting ligands for precise/specific targeting and other biological uses. Using functionalised biomacromolecules such as short chained peptides, helps in improving pharmacokinetic properties and biodistribution profile of the drug. Apart from this, functionalised SP are being employed as cell penetrating peptides and prodrug to specifically and selectively target tumor sites. In order to minimize any unwanted interaction and adverse effects, the stability and safety of SP should be ensured throughout its development from manufacturing to market. Formulation development and characterization strategies of these potential molecules are described in the following review along with various applications and details of marketed formulations.

Self-Assembled Nanoparticles with Well-Defined Oligosaccharide Promote Osteogenesis by Regulating Golgi Stress Response

Osteoporosis, a prevalent disease characterized by low bone density and increased fracture risk, poses significant health challenges for the elderly. Current treatments offer short-term benefits but are limited by long-term efficacy and adverse effects, highlighting the need for new strategies. Chondroitin sulfate polysaccharides (CS), a major component of the bone matrix, are crucial for bone and cartilage health. However, their role in osteoporosis is understudied due to the heterogeneity of natural CS. we found reduced CS levels in osteoporosis patients and developed CS4-NP, a self-assembled tetrasaccharide nanoparticle that mimics CS's structure. CS4-NP, which efficiently delivers the active CS4, significantly improves bone mass in ovariectomized osteoporosis models. It activates the Activating Transcription Factor 4-Cystathionine gamma-Lyase signaling axis in pre-osteoblasts, enhancing osteogenesis. our findings suggest that CS4-NP, an oligosaccharide-based nanomaterial, could address the limitations of current treatments and provide a viable strategy for osteoporosis.

Cathepsin K-Positive Cell Lineage Promotes In Situ Dentin Formation Controlled by Nociceptive Sonic Hedgehog

Oral diseases affect nearly half of the global population throughout their lifetime causing pain, as estimated by the World Health Organization. Preservation of vital pulp is the therapeutic core as well as a challenge to protect natural teeth. Current bottleneck lies in that the regenerative capacity of injured pulp is undetermined. In this study, we identified a lifelong lineage that is labelled by cathepsin K (Ctsk) contributing to the physiological, reactionary and reparative odontogenesis of mouse molars. Ctsk+ cell-mediated dentin formation is regulated by nociceptive nerve-derived Sonic Hedgehog (Shh), especially rapidly responsive to acute injury. Notably, exogenous Shh protein to the injury pulp can preserve Ctsk+ cell capacity of odontogenesis for the nearby crown pulp and even remote root apex growth, alleviating conventionally developmental arrest in youth pulpitis. Exposed to chronical attrition, aged pulp Ctsk+ cells still hold the capacity to respond to acute stimuli and promote reparative odontogenesis, also enhanced by exogenous Shh capping. Therefore, Ctsk+ cells may be one of the lineages for accelerating precision medicine for efficient pulp treatment across ages. Shh application can be a candidate for vital pulp preservation and pulp injury repair by promoting regenerative odontogenesis to a certain extent from young adults to older individuals.

The role and future prospects of artificial intelligence algorithms in peptide drug development

Peptide medications have been more well-known in recent years due to their many benefits, including low side effects, high biological activity, specificity, effectiveness, and so on. Over 100 peptide medications have been introduced to the market to treat a variety of illnesses. Most of these peptide medications are developed on the basis of endogenous peptides or natural peptides, which frequently required expensive, time-consuming, and extensive tests to confirm. As artificial intelligence advances quickly, it is now possible to build machine learning or deep learning models that screen a large number of candidate sequences for therapeutic peptides. Therapeutic peptides, such as those with antibacterial or anticancer properties, have been developed by the application of artificial intelligence algorithms.The process of finding and developing peptide drugs is outlined in this review, along with a few related cases that were helped by AI and conventional methods. These resources will open up new avenues for peptide drug development and discovery, helping to meet the pressing needs of clinical patients for disease treatment. Although peptide drugs are a new class of biopharmaceuticals that distinguish them from chemical and small molecule drugs, their clinical purpose and value cannot be ignored. However, the traditional peptide drug research and development has a long development cycle and high investment, and the creation of peptide medications will be substantially hastened by the AI-assisted (AI+) mode, offering a new boost for combating diseases.

Enhanced Bone Regeneration through Regulation of Mechanoresponsive FAK-ERK1/2 Signaling by ZINC40099027 during Distraction Osteogenesis

Background: Focal adhesion kinase (FAK) is activated by mechanical stimulation and plays a vital role in distraction osteogenesis (DO), a well-established but lengthy procedure for repairing large bone defects. Both angiogenesis and osteogenesis contribute to bone regeneration during DO. However, the effects of ZINC40099027 (ZN27), a potent FAK activator, on angiogenesis, osteogenesis, and bone regeneration in DO remain unknown. Methods: The angiogenic potential of human umbilical vein endothelial cells (HUVECs) was evaluated using transwell migration and tube formation assays. The osteogenic activity of bone marrow mesenchymal stem cells (BMSCs) was assessed using alkaline phosphatase (ALP) and alizarin red s (ARS) staining. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR), western blot, and immunofluorescence staining were used to assay angiogenic markers, osteogenic markers, and FAK-extracellular signal-regulated kinase 1/2 (ERK1/2) signaling. In vivo, a rat tibia DO model was established to verify the effects of ZN27 on neovascularization and bone regeneration using radiological and histological analyses. Results: ZN27 promoted the migration and angiogenesis of HUVECs. Additionally, ZN27 facilitated the osteogenic differentiation of BMSCs, as revealed by increased ALP activity, calcium deposition, and expression of osteogenesis-specific markers. The ERK1/2-specific inhibitor PD98059 significantly hindered the effects of ZN27, suggesting the participation of FAK-ERK1/2 signaling in ZN27-enhanced angiogenesis and osteogenesis. As indicated by improved radiological and histological features, ZN27 induced active angiogenesis within the distraction area and accelerated bone regeneration in a rat DO model. Conclusion: Our results show that ZN27 targets FAK-ERK1/2 signaling to stimulate both angiogenesis and osteogenesis, and ZN27 accelerates bone regeneration in DO, suggesting the therapeutic potential of ZN27 for repairing large bone defects in the mechanobiological environment during DO.

Ultrasound-triggered biomimetic ultrashort peptide nanofiber hydrogels promote bone regeneration by modulating macrophage and the osteogenic immune microenvironment

The immune microenvironment plays a vital role in bone defect repair. To create an immune microenvironment that promotes osteogenesis, researchers are exploring ways to enhance the differentiation of M2-type macrophages. Functional peptides have been discovered to effectively improve this process, but they are limited by low efficiency and rapid degradation in vivo. To overcome these issues, peptide with both M2 regulatory and self-assembly modules was designed as a building block to construct an ultrasound-responsive nanofiber hydrogel. These nanofibers can be released from hydrogel in a time-dependent manner upon ultrasound stimulation, activating mitochondrial glycolytic metabolism and the tricarboxylic acid cycle, inhibiting reactive oxygen species production and enhancing M2 macrophage polarization. The hydrogel exhibits advanced therapeutic potential for bone regeneration by triggering M2 macrophages to secrete BMP-2 and IGF-I, accelerating the differentiation of bone marrow mesenchymal stem cells (BMSCs) into osteoblasts. Thus, modularly designed biomimetic ultrashort peptide nanofiber hydrogels provide a novel strategy to rebuild osteogenic immune microenvironments for bone repair.

Modification of the small intestinal submucosa membrane with oligopeptides screened from intrinsically disordered regions to promote angiogenesis and accelerate wound healing

A slow vascularization rate is considered one of the major disadvantages of biomaterials used for accelerating wound healing. Several efforts, including cellular and acellular technologies, have been made to facilitate biomaterial-induced angiogenesis. However, no well-established techniques for promoting angiogenesis have been reported. In this study, a small intestinal submucosa (SIS) membrane modified by an angiogenesis-promoting oligopeptide (QSHGPS) screened from intrinsically disordered regions (IDRs) of MHC class II was used to promote angiogenesis and accelerate wound healing. Because the main component of SIS membranes is collagen, the collagen-binding peptide sequence TKKTLRT and the pro-angiogenic oligopeptide sequence QSHGPS were used to construct chimeric peptides to obtain specific oligopeptide-loaded SIS membranes. The resulting chimeric peptide-modified SIS membranes (SIS-L-CP) significantly promoted the expression of angiogenesis-related factors in umbilical vein endothelial cells. Furthermore, SIS-L-CP exhibited excellent angiogenic and wound-healing abilities in a mouse hindlimb ischaemia model and a rat dorsal skin defect model. The high biocompatibility and angiogenic capacity of the SIS-L-CP membrane make it promising in angiogenesis- and wound healing-related regenerative medicine.