Peptide System Research Articles

Unravelling heparin's enhancement of amyloid aggregation in a model peptide system.

A coarse-grained (CG) model for heparin, an anionic polysaccharide, was developed to investigate the mechanisms of heparin's enhancement of fibrillation in many amyloidogenic peptides. CG molecular dynamics simulations revealed that heparin, by forming contacts with the model amyloidogenic peptide, amyloid-β's K16LVFFAE22 fragment (Aβ16-22), promoted long-lived and highly beta-sheet-like domains in the peptide oligomers. Concomitantly, heparin-Aβ16-22 contacts suppressed the entropy of mixing of the oligomers' beta-domains. Such oligomers could make better seeds for fibrillation, potentially contributing to heparin's fibril-enhancing behaviour. Additionally, reductions in heparin's flexibility led to delayed aggregation, and less ordered Aβ16-22 oligomers, thus offering insights into the contrasting inhibition of fibrillation by the relatively rigid polysaccharide, chitosan.

Intrinsically disordered Prosystemin discloses biologically active repeat motifs

The in-depth studies over the years on the defence barriers by tomato plants have shown that the Systemin peptide controls the response to a wealth of environmental stress agents. This multifaceted stress reaction seems to be related to the intrinsic disorder of its precursor protein, Prosystemin (ProSys). Since latest findings show that ProSys has biological functions besides Systemin sequence, here we wanted to assess if this precursor includes peptide motifs able to trigger stress-related pathways. Candidate peptides were identified in silico and synthesized to test their capacity to trigger defence responses in tomato plants against different biotic stressors. Our results demonstrated that ProSys harbours several repeat motifs which triggered plant immune reactions against pathogens and pest insects. Three of these peptides were detected by mass spectrometry in plants expressing ProSys, demonstrating their effective presence in vivo. These experimental data shed light on unrecognized functions of ProSys, mediated by multiple biologically active sequences which may partly account for the capacity of ProSys to induce defense responses to different stress agents.

Encapsulation of a novel peptide derived from histatin-1 in liposomes against initial enamel caries in vitro and in vivo.

Biomimetic mineralization mediated by proteins and peptides is a promising strategy for enamel repair, and its specific application model needs more research. In this work, we exploited a liposomal delivery system for a novel peptide (DK5) derived from histatin-1 (DK5-Lips) as a new biomimetic mineralization strategy against initial enamel caries. The DK5-Lips was prepared using calcium acetate gradient method and then the in vitro release, salivary stability, and cytotoxicity were studied. Initial enamel caries was created in bovine enamel blocks and subjected to pH-cycling model treated with DK5-Lips. Surface microhardness testing, polarized light microscopy (PLM), and transverse microradiography (TMR) were analyzed. Then the biocompatibility of DK5-Lips was evaluated in the caries model of Sprague-Dawley rats, and the anti-caries effect was assessed using Micro-CT analysis, Keyes scores, and PLM in vivo. DK5-Lips provided a mean particle size of (97.63 ± 4.94)nm and encapsulation efficiency of (61.46 ± 1.44)%, exhibiting a sustained release profile, excellent stability in saliva, and no significant toxicity on human gingival fibroblasts (HGFs). The DK5-Lips group had higher surface microhardness recovery, shallower caries depth, and less mineral loss in bovine enamel. Animal experiments showed higher volume and density values of residual molar enamel, lower Keyes score, and shallower lesion depth of the DK5-Lips group with good biocompatibility. As a safe and effective application model, DK5-Lips could significantly promote the remineralization of initial enamel caries both in vitro and in vivo. The potential of liposome utilization as vehicle for oral delivery of functional peptides may provide a new way for enamel restoration.

Chronopharmacokinetic and Metabolites Investigations of the Cardiovascular Drugs Perindopril

The heart and vascular systems are well-coordinated. There is a noticeable uneven distribution of regulatory mechanisms and pathogenic events over the course of a day. In addition, the physiological circadian clock of the cardiovascular system might be disrupted by several disorders. In terms of global mortality and morbidity, heart failure (HF) ranks high. The angiotensin receptor-neprilysin inhibitor perindopril is now a valid option for treating heart failure. There is a lack of comprehensive evaluations of perindopril’s safety and effectiveness in HF at the present time. First, we provided an overview of perindopril’s pharmacological actions, which include inhibiting the renin-angiotensin system and decreasing natriuretic peptide breakdown in the natriuretic peptide system. After that, we summed up the benefits of perindopril for heart failure patients with preserved ejection fraction (HFpEF) or reduced ejection fraction (HFrEF), such as lowering the risk of death and hospitalization, reversing cardiac remodeling, regulating biomarkers of heart failure, improving quality of life, providing antiarrhythmic effects, enhancing renal dysfunction, and regulating metabolism. Our discussion of perindopril’s safety and tolerability in treating HFrEF or HFpEF came to a close. Although there is a considerable risk of hypotension, perindopril demonstrated superior safety and tolerability when compared with placebo. For HFrEF patients, perindopril is a safe and effective therapy option, however, for HFpEF patients, it shows little benefit, according to the majority of studies. Soon, perindopril will likely be one of the most effective drugs available to treat heart failure.

Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations.

Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneous organization of two different peptides into a supramolecular architecture. Here we use molecular dynamics simulations to quantify the effect of anionic amino acid type on co-assembly dynamics and nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide sequences follow a general pattern: CQCFCFCFCQC, where all C's are either a positively charged or a negatively charged amino acid. Specifically, we investigate the effect of substituting aspartic acid residues for the glutamic acid residues in the established CATCH(6E-) molecule, while keeping CATCH(6K+) unchanged. Our results show that structures consisting of CATCH(6K+) and CATCH(6D-) form flatter β-sheets, have stronger interactions between charged residues on opposing β-sheet faces, and have slower co-assembly kinetics than structures consisting of CATCH(6K+) and CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics and fibrillar structure can help guide the development of advanced biomaterials and grant insight into sequence-to-structure relationships.

Sympathetic Neurotransmitter, VIP, Delays Intervertebral Disc Degeneration via FGF18/FGFR2-Mediated Activation of Akt Signaling Pathway.

Neuromodulation-related intervertebral disc degeneration (IVDD) is a novel IVDD pattern and are proposed recently. However, the mechanistic basis of neuromodulation and intervertebral disc (IVD) homeostasis remains unclear. Here, this study aimed to investigate the expression of postganglionic sympathetic nerve fiber-derived vasoactive intestinal peptide (VIP) system in human IVD tissue, and to assess the role of VIP-related neuromodulation in IVDD. Patient samples and in vitro cell experiments showed that the expression of receptors for VIP is negatively correlated with the severity of IVDD, and the administration of exogenous VIP can ameliorate interleukin 1β-induced nucleus pulposus (NP) cell apoptosis and inflammation. Further mRNA-seq analysis revealed that fibroblast growth factor 18- (FGF18)-mediated activation of V-akt murine thymoma viral oncogene homolog signaling pathway is involved in the protective effects of VIP on inflammation-induced NP cell degeneration. Further analysis identified VIP via its receptor vasoactive intestinal peptide receptor 2 can directly result in decreased expression of miR-15a-5p, which targeted FGF18. Finally, in vivo mice lumbar IVDD model confirmed that focally exogenous administration of VIP can effectively ameliorated the progression of IVDD, as shown by the radiological and histological analysis. In conclusion, these results indicated that sympathetic neurotransmitter, VIP, delayed IVDD via FGF18/FGFR2-mediated activation of V-akt murine thymoma viral oncogene homolog signaling pathway, which will broaden the horizon concerning how the neuromodulation correlates with IVDD and shed new light on novel therapeutical alternatives to IVDD.

Colon-targeted S100A8/A9-specific peptide systems ameliorate colitis and colitis-associated colorectal cancer in mouse models.

The link between chronic inflammation and cancer development is well acknowledged. Inflammatory bowel disease including ulcerative colitis and Crohn's disease frequently promotes colon cancer development. Thus, control of intestinal inflammation is a therapeutic strategy to prevent and manage colitis-associated colorectal cancer (CRC). Recently, gut mucosal damage-associated molecular patterns S100A8 and S100A9, acting via interactions with their pattern recognition receptors (PRRs), especially TLR4 and RAGE, have emerged as key players in the pathogenesis of colonic inflammation. We found elevated serum levels of S100A8 and S100A9 in both colitis and colitis-associated CRC mouse models along with significant increases in their binding with PRR, TLR4, and RAGE. In this study we developed a dual PRR-inhibiting peptide system (rCT-S100A8/A9) that consisted of TLR4- and RAGE-inhibiting motifs derived from S100A8 and S100A9, and conjugated with a CT peptide (TWYKIAFQRNRK) for colon-specific delivery. In human monocyte THP-1 and mouse BMDMs, S100A8/A9-derived peptide comprising TLR4- and RAGE-interacting motif (0.01, 0.1, 1 μM) dose-dependently inhibited the binding of S100 to TLR4 or RAGE, and effectively inhibited NLRP3 inflammasome activation. We demonstrated that rCT-S100A8/A9 had appropriate drug-like properties including in vitro stabilities and PK properties as well as pharmacological activities. In mouse models of DSS-induced acute and chronic colitis, injection of rCT-S100A8/A9 (50 μg·kg-1·d-1, i.p. for certain consecutive days) significantly increased the survival rates and alleviated the pathological injuries of the colon. In AOM/DSS-induced colitis-associated colorectal cancer (CAC) mouse model, injection of rCT-S100A8/A9 (50 μg·kg-1·d-1, i.p.) increased the body weight, decreased tumor burden in the distal colon, and significantly alleviated histological colonic damage. In mice bearing oxaliplatin-resistant CRC xenografts, injection of rCT-S100A8/A9 (20 μg/kg, i.p., every 3 days for 24-30 days) significantly inhibited the tumor growth with reduced EMT-associated markers in tumor tissues. Our results demonstrate that targeting the S100-PRR axis improves colonic inflammation and thus highlight this axis as a potential therapeutic target for colitis and CRC.

Abstract C113: Discovery of a novel auristatin antibody drug conjugate drug linker with equal efficacy and reduced bone marrow toxicity compared to vedotin

Abstract There are four vedotin drug linker containing antibody drug conjugates currently approved for treating cancer patients, proving that this technology platform is an effective modality for the treatment of both hematologic and solid tumors. The primary mechanism of vedotin ADCs, direct cytotoxicity, is the result of intracellular release of monomethyl auristatin E (MMAE) after cleavage of the valine-citrulline (Val-Cit) dipeptide by lysosomal proteases. However, off-tumor delivery of MMAE can result in dose limiting bone marrow toxicity in preclinical models. Maintaining potency in cancer cells while reducing the bone marrow toxicity of vedotin ADCs could allow higher or more frequent clinical dosing and potentially improved response rates and patient outcomes. To decrease bone marrow toxicity of MMAE empowered ADCs, we developed a process to identify peptidic linker systems that provide selectivity for cancer cells over bone marrow cells. From this process we identified a tripeptide sequence (D-leucine-alanine-glutamate, dLAE) that is preferentially cleaved in cancer cells and used it to develop a drug linker that releases MMAE upon cleavage of this tripeptide. Here, we present in vitro and in vivo data comparing ADCs containing vedotin and dLAE tripeptide drug linkers. While ADCs with the dLAE drug linker had comparable in vitro cytotoxicity and antitumor activity to vedotin, the dLAE ADCs had a higher maximum tolerated dose in exploratory rat and cynomolgus macaque toxicity studies due to a reduction in bone marrow toxicity. Reduced bone marrow toxicity was correlated with decreased linker catabolism in bone marrow cells for conjugates bearing the dLAE tripeptide compared to Val-Cit, while similar catabolism was observed in cancer cells. Together, these preclinical data highlight that changing the peptide of the vedotin drug linker from Val-Cit to dLAE can yield ADCs with an improved preclinical therapeutic window. Given the preclinical characteristics of the dLAE drug linker, a clinical trial is being planned to evaluate an anti-CD30 ADC (SGN-35T). Citation Format: Noah A Bindman, Roma Yumul, Erica E McKinney, Scott Blackburn, Nicole Blesie, Xinqun Zhang, Brendan Drouhard, Sarah Anderson, Calvin Neace, David Ortiz, KC Crowder, Nancy Everds, Chris Carosino, Forgivemore Magunda, Django Sussman, Esther Trueblood, Nicole M. Okeley, Peter Senter. Discovery of a novel auristatin antibody drug conjugate drug linker with equal efficacy and reduced bone marrow toxicity compared to vedotin [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C113.

Peptide Amphiphiles as Biodegradable Adjuvants for Efficient Retroviral Gene Delivery.

Retroviral gene delivery is the key technique for in vitro and ex vivo gene therapy. However, inefficient virion-cell attachment resulting in low gene transduction efficacy remains a major challenge in clinical applications. Adjuvants for ex vivo therapy settings need to increase transduction efficiency while being easily removed or degraded post-transduction to prevent the risk of venous embolism after infusing the transduced cells back to the bloodstream of patients, yet no such peptide system have been reported thus far. In this study, peptide amphiphiles (PAs) with a hydrophobic fatty acid and a hydrophilic peptide moiety that reveal enhanced viral transduction efficiency are introduced. The PAs form β-sheet-rich fibrils that assemble into positively charged aggregates, promoting virus adhesion to the cell membrane. The block-type amphiphilic sequence arrangement in the PAs ensures efficient cell-virus interaction and biodegradability. Good biodegradability is observed for fibrils forming small aggregates and it isshown that via molecular dynamics simulations, the fibril-fibril interactions of PAs are governed by fibril surface hydrophobicity. These findings establish PAs as additives in retroviral gene transfer, rivalling commercially available transduction enhancers in efficiency and degradability with promising translational options in clinical gene therapy applications.

Herbal medicine (Oryeongsan) for fluid and sodium balance in renal cortex of spontaneously hypertensive rats

BackgroundHerbal medicine Oryeongsan (ORS), also known as Wulingsan in Chinese, has been used for the treatment of impaired body fluid balance. However, the mechanisms involved are not clearly defined. The purpose of the present study was to identify the actions of ORS on the renal excretory function and blood pressure (BP) and to define the mechanisms involved in association with renin-angiotensin system (RAS) and natriuretic peptide system (NPS) in spontaneously hypertensive rats (SHR), an animal model of human essential hypertension. MethodsChanges in urine volume (UV), excretion of electrolytes including Na+ (urinary excretion of Na+ (UNaV)) were measured. RT-PCR was performed to trace the changes in expression of RAS, NPS and sodium (Na+)-hydrogen (H+) exchanger 3 (NHE3) in the renal cortex. ResultsIn the SHR treated with vehicle (SHR-V) group, UV and UNaV were suppressed and the Na+ balance was maintained at the higher levels leading to an increase in BP compared to WKY-V group. These were accompanied by an increase in NHE3 expression with an accentuation of angiotensin I converting enzyme-angiotensin II type 1 (ACE-AT1) receptor and concurrent suppression of angiotensin II type 2 (AT2) receptor/ACE2-Mas receptor expression in the renal cortex. Chronic treatment with ORS increased UV and UNaV, and decreased the Na+ and water balance with a decrease in BP in the ORS-treated SHR-ORS group compared to SHR-V. These were accompanied by a decrease in NHE3 expression with a suppression of ACE-AT1 receptor and concurrent accentuation of AT2/ACE2-Mas receptor. ConclusionThe present study shows that ORS reduced BP with a decrease in Na+ and water retention by a suppression of NHE3 expression via modulation of RAS and NPS in SHR. The present study provides pharmacological rationale for the treatment of hypertension with ORS in SHR.

Progesterone distribution in the trigeminal system and its role to modulate sensory neurotransmission: influence of sex

BackgroundWomen are disproportionately affected by migraine, representing up to 75% of all migraine cases. This discrepancy has been proposed to be influenced by differences in hormone levels between the sexes. One such hormone is progesterone. Calcitonin gene-related peptide (CGRP) system is an important factor in migraine pathophysiology and could be influenced by circulating hormones. The purpose of this study was to investigate the distribution of progesterone and its receptor (PR) in the trigeminovascular system, and to examine the role of progesterone to modulate sensory neurotransmission.MethodsTrigeminal ganglion (TG), hypothalamus, dura mater, and the basilar artery from male and female rats were carefully dissected. Expression of progesterone and PR proteins, and mRNA levels from TG and hypothalamus were analyzed by immunohistochemistry and real-time quantitative PCR. CGRP release from TG and dura mater were measured using an enzyme-linked immunosorbent assay. In addition, the vasomotor effect of progesterone on male and female basilar artery segments was investigated with myography.ResultsProgesterone and progesterone receptor -A (PR-A) immunoreactivity were found in TG. Progesterone was located predominantly in cell membranes and in Aδ-fibers, and PR-A was found in neuronal cytoplasm and nucleus, and in satellite glial cells. The number of positive progesterone immunoreactive cells in the TG was higher in female compared to male rats. The PR mRNA was expressed in both hypothalamus and TG; however, the PR expression level was significantly higher in the hypothalamus. Progesterone did not induce a significant change neither in basal level nor upon stimulated release of CGRP from dura mater or TG in male or female rats when compared to the vehicle control. However, pre-treated with 10 µM progesterone weakly enhanced capsaicin induced CGRP release observed in the dura mater of male rats. Similarly, in male basilar arteries, progesterone significantly amplified the dilation in response to capsaicin.ConclusionsIn conclusion, these results highlight the potential for progesterone to modulate sensory neurotransmission and vascular responses in a complex manner, with effects varying by sex, tissue type, and the nature of the stimulus. Further investigations are needed to elucidate the underlying mechanisms and physiological implications of these findings.Graphical

Abstract 14022: N-terminal Prohormone of B-type Natriuretic Peptide Levels Partly Mediate the Relationship of Advanced Hepatic Fibrosis With Mortality in Coronary Artery Disease

Background Advanced hepatic fibrosis (AHF) is associated with cardiac remodeling and adverse outcomes in patients with coronary artery disease (CAD). The mechanistic basis of this relationship and the contribution of the natriuretic peptide system is unclear. Hypothesis: The association of AHF with mortality in CAD is mediated by circulating N-terminal prohormone of B-type natriuretic peptide (NTproBNP) level. Methods: Patients undergoing cardiac catheterization for evaluation of CAD were enrolled in the Emory Cardiovascular Biobank and those with acute myocardial infarction, cirrhosis, and hepatocellular carcinoma were excluded. Plasma NTproBNP was measured, and Fibrosis-4 (FIB-4) index was calculated using age, alanine aminotransferase, aspartate aminotransferase, and platelet count. FIB-4 ≥2.67 was used to define AHF. Association of AHF and NTproBNP with all-cause mortality was studied using multivariable-adjusted Cox models and mediation analyses. Results: Study population included 3,432 patients with mean age 65 y and among them 32% were women, 24% were Black, and 15% had AHF. Median NTproBNP level was 2.5-fold higher among those with AHF (572, 95% CI 225-2203 pg/ml) compared with those without (223, 95% CI 93-689 pg/ml). AHF was independently associated with 49% higher all-cause mortality in multivariable-adjusted Cox models [HR(95% CI): 1.49 (1.26-1.77)]. NTproBNP stratified mortality risk associated with AHF ( Figure ). Patients with AHF and high NTproBNP (≥300 pg/ml) were at the highest risk, while risk in AHF and low NTproBNP (<300 pg/ml) group was similar to those without AHF and low NTproBNP. NTproBNP was independently associated with mortality risk and mediated 61% of the effect of AHF on mortality in causal mediation analysis. Conclusion: NTproBNP partly mediates the excess mortality associated with AHF in patients with CAD. Therapeutic strategies targeting the natriuretic peptide system may help improve outcomes in this high-risk group.

Neutron reflection and scattering in characterising peptide assemblies

Self-assemblies of de novo designed short peptides at interface and in bulk solution provide potential platforms for developing applications in many medical and technological areas. However, characterising how bioinspired supramolecular nanostructures evolve with dynamic self-assembling processes and respond to different stimuli remains challenging. Neutron scattering technologies including small angle neutron scattering (SANS) and neutron reflection (NR) can be advantageous and complementary to other state-of-the-art techniques in tracing structural changes under different conditions. With more neutron sources now available, SANS and NR are becoming increasingly popular in studying self-assembling processes of diverse peptide and protein systems, but the difficulty in experimental manipulation and data analysis can deter beginners. This review will introduce the basic theory, general experimental setup and data analysis of SANS and NR, followed by provision of their applications in characterising interfacial and solution self-assemblies of representative peptides and proteins. SANS and NR are remarkably effective in determining the morphological features self-assembled short peptides, especially size and shape transitions as a result of either sequence changes or in response to environmental stimuli, demonstrating the unique capability of NR and SANS in unravelling the interactive processes. These examples highlight the potential of NR and SANS in supporting the development of novel short peptides and proteins as biopharmaceutical candidates in the fight against many diseases and infections that share common features of membrane interactive processes.

A dual drug-loaded peptide system with morphological transformation prolongs drug retention and inhibits breast cancer growth

The treatment of breast cancer relies heavily on chemotherapy, but chemotherapy is limited by the disadvantages of poor targeting, susceptibility to extracellular matrix (ECM) interference and a short duration of action in tumor cells. To address these limitations, we developed an amphipathic peptide containing an RGD motif, Pep1, that encapsulated paclitaxel (PTX) and losartan potassium (LP) to form the drug-loaded peptide PL/Pep1. PL/Pep1 self-assembled into spherical nanoparticles (NPs) under normal physiological conditions and transformed into aggregates containing short nanofibers at acidic pH. The RGD peptide facilitated tumor targeting and the aggregates prolonged drug retention in the tumor, which allowed more drug to reach and accumulate in the tumor tissue to promote apoptosis and remodel the tumor microenvironment. The results of in vitro and in vivo experiments confirmed the superiority of PL/Pep1 in terms of targeting, prolonged retention and facilitated penetration for antitumor therapy. In conclusion, amphipathic peptides as coloaded drug carriers are a new platform and strategy for breast cancer chemotherapy.

The molecular dynamics simulation of peptide-based structure adsorption inside nanochannel with surface roughness

Peptides result from partial hydrolysis of protein polypeptide chains. These atomic structures are the main section of various protein compounds. So, the adsorption process of these structures can be used in various medical applications. The small peptide structure is absorbed using a platinum nanochannel with cubic roughness in an aqueous environment in the present computational examination. Technically, the simulation of the nanochannel- peptide system is done using the Molecular Dynamics (MD) method. The different atoms' interactions in our systems are defined by DREIDING/Universal Force-Field (UFF), TIP3P, and Embedded Atom Model (EAM). Temperature, total energy (TE), Radial Distribution Function (RDF), profiles of density/velocity/temperature, absorption ratio, interaction energy, and volume were presented for t = 30 ns in order to provide a physical description of the peptide adsorption process. Our simulation results show the atomic stability of P-nanochannel system in the attendance of H2O molecules. Moreover, peptide absorption ratio inside the MD box reached a 78 % value. This result shows the appropriate behavior of a metallic nanochannel with rectangular roughness to adsorption of various protein-based structures, such as Ps for medical aims.

Evaluation of Hydrogen-Deuterium Exchange during Transient Vapor Binding of MeOD with Model Peptide Systems Angiotensin II and Bradykinin.

The advancement of hybrid mass spectrometric tools as an indirect probe of molecular structure and dynamics relies heavily upon a clear understanding between gas-phase ion reactivity and ion structural characteristics. This work provides new insights into gas-phase ion-neutral reactions of the model peptides (i.e., angiotensin II and bradykinin) on a per-residue basis by integrating hydrogen/deuterium exchange, ion mobility, tandem mass spectrometry, selective vapor binding, and molecular dynamics simulations. By comparing fragmentation patterns with simulated probabilities of vapor uptake, a clear link between gas-phase hydrogen/deuterium exchange and the probabilities of localized vapor association is established. The observed molecular dynamics trends related to the sites and duration of vapor binding track closely with experimental observation. Additionally, the influence of additional charges and structural characteristics on exchange kinetics and ion-neutral cluster formation is examined. These data provide a foundation for the analysis of solvation dynamics of larger, native-like conformations of proteins in the gas phase.

Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments

The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3–12 m<sc>m</sc>) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 m<sc>m</sc> of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.

Deep Learning Empowers the Discovery of Self-Assembling Peptides with Over 10 Trillion Sequences.

Self-assembling of peptides is essential for a variety of biological and medical applications. However, it is challenging to investigate the self-assembling properties of peptides within the complete sequence space due to the enormous sequence quantities. Here, it is demonstrated that a transformer-based deep learning model is effective in predicting the aggregation propensity (AP) of peptide systems, even for decapeptide and mixed-pentapeptide systems with over 10 trillion sequence quantities. Based on the predicted AP values, not only the aggregation laws for designing self-assembling peptides are derived, but the transferability relation among the APs of pentapeptides, decapeptides, and mixed pentapeptides is also revealed, leading to discoveries of self-assembling peptides by concatenating or mixing, as consolidated by experiments. This deep learning approach enables speedy, accurate, and thorough search and design of self-assembling peptides within the complete sequence space of oligopeptides, advancing peptide science by inspiring new biological and medical applications.

Comprehensive Regulation of Liquid-Liquid Phase Separation of Polypeptides.

The elucidation of the molecular driving forces responsible for Liquid-liquid Phase Separation (LLPS) of proteins and nucleic acids within living cells is crucial for understanding its biological functions and its role in related diseases. In the present study, we investigated the regulation of LLPS in a series of polypeptides with repetitive proline and arginine (PR) sequences by modifying their length and the salt concentration in the solution. Our findings indicate that higher salt concentrations are necessary for LLPS of repetitive PR peptides longer than eight PRs, which emerges as a threshold value. To pinpoint the molecular forces driving the LLPS in peptides, we sequentially introduced various concentrations of hydrophobic disruptors, such as 1,6-hexanediol, and electrostatic regulators, such as ethyl alcohol and 6-Aminocaproic acid. We further modulated the electrostatic interaction by introducing ethyl alcohol and 6-Aminocaproic acid to alter the dielectric constant of the solution. The inclusion of ethyl alcohol intensified the electrostatic interaction between arginine molecules, facilitating LLPS of PR15, while 6-Aminocaproic acid yielded the reverse effect. We deduced that the phase separation in peptide systems is conjointly driven by hydrophobicity and electrostatic interactions. These insights can guide the regulation of LLPS in other peptide and protein systems, and could be pivotal in addressing abnormal aggregations of proteins and nucleic acids.

Mechanisms of acupuncture-electroacupuncture on inflammatory pain.

Acupuncture, as a traditional treatment, has been extensively used in China for thousands of years. According to the World Health Organization (WHO), acupuncture is recommended for the treatment of 77 diseases. And sixteen of these diseases are related to inflammatory pain. As a combination of traditional acupuncture and modern electrotherapy, electroacupuncture (EA) has satisfactory analgesic effects on various acute and chronic pain. Because of its good analgesic effects and no side effects, acupuncture has been widely accepted all over the world. Despite the increase in the number of studies, the mechanisms via which acupuncture exerts its analgesic effects have not been conclusively established. A literature review of related research is of great significance to elaborate on its mechanisms and to inform on further research directions. We elucidated on its mechanisms of action on inflammatory pain from two levels: peripheral and central. It includes the mechanisms of acupuncture in the periphery (immune cells and neurons, purinergic pathway, nociceptive ion channel, cannabinoid receptor and endogenous opioid peptide system) and central nervous system (TPRV1, glutamate and its receptors, glial cells, GABAergic interneurons and signaling molecules ). In this review, we collected relevant recent studies to systematically explain the mechanisms of acupuncture in treating inflammatory pain, with a view to providing direction for future applications of acupuncture in inflammatory pain and promoting clinical development.