Flexible scaffold-based cheminformatics approach for polypharmacological drug design.

Effective treatments for complex central nervous system (CNS) disorders require drugs with polypharmacology and multifunctionality, yet designing such drugs remains a challenge. Here, we present a flexible scaffold-based cheminformatics approach (FSCA) for the rational design of polypharmacological drugs. FSCA involves fitting a flexible scaffold to different receptors using different binding poses, as exemplified by IHCH-7179, which adopted a "bending-down" binding pose at 5-HT2AR to act as an antagonist and a "stretching-up" binding pose at 5-HT1AR to function as an agonist. IHCH-7179 demonstrated promising results in alleviating cognitive deficits and psychoactive symptoms in mice by blocking 5-HT2AR for psychoactive symptoms and activating 5-HT1AR to alleviate cognitive deficits. By analyzing aminergic receptor structures, we identified two featured motifs, the "agonist filter" and "conformation shaper," which determine ligand binding pose and predict activity at aminergic receptors. With these motifs, FSCA can be applied to the design of polypharmacological ligands at other receptors.

5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.

Drugs frequently require interactions with multiple targets-via a process known as polypharmacology-to achieve their therapeutic actions. Currently, drugs targeting several serotonin receptors, including the 5-HT2C receptor, are useful for treating obesity, drug abuse, and schizophrenia. The competing challenges of developing selective 5-HT2C receptor ligands or creating drugs with a defined polypharmacological profile, especially aimed at G protein-coupled receptors (GPCRs), remain extremely difficult. Here, we solved two structures of the 5-HT2C receptor in complex with the highly promiscuous agonist ergotamine and the 5-HT2A-C receptor-selective inverse agonist ritanserin at resolutions of 3.0 Å and 2.7 Å, respectively. We analyzed their respective binding poses to provide mechanistic insights into their receptor recognition and opposing pharmacological actions. This study investigates the structural basis of polypharmacology at canonical GPCRs and illustrates how understanding characteristic patterns of ligand-receptor interaction and activation may ultimately facilitate drug design at multiple GPCRs.

Serotonin 2A Receptor (5-HT2AR) Agonists: Psychedelics and Non-Hallucinogenic Analogues as Emerging Antidepressants.

Psychedelics make up a group of psychoactive compounds that induce hallucinogenic effects by activating the serotonin 2A receptor (5-HT2AR). Clinical trials have demonstrated the traditional psychedelic substances like psilocybin as a class of rapid-acting and long-lasting antidepressants. However, there is a pressing need for rationally designed 5-HT2AR agonists that possess optimal pharmacological profiles in order to fully reveal the therapeutic potential of these agonists and identify safer drug candidates devoid of hallucinogenic effects. This Perspective provides an overview of the structure-activity relationships of existing 5-HT2AR agonists based on their chemical classifications and discusses recent advancements in understanding their molecular pharmacology at a structural level. The encouraging clinical outcomes of psychedelics in depression treatment have sparked drug discovery endeavors aimed at developing novel 5-HT2AR agonists with improved subtype selectivity and signaling bias properties, which could serve as safer and potentially nonhallucinogenic antidepressants. These efforts can be significantly expedited through the utilization of structure-based methods and functional selectivity-directed screening.

Leveraging intracellular ALDH1A1 activity for selective cancer stem-like cell labeling and targeted treatment via in vivo click reaction.

Inhibition of overexpressed enzymes is among the most promising approaches for targeted cancer treatment. However, many cancer-expressed enzymes are "nonlethal," in that the inhibition of the enzymes' activity is insufficient to kill cancer cells. Conventional antibody-based therapeutics can mediate efficient treatment by targeting extracellular nonlethal targets but can hardly target intracellular enzymes. Herein, we report a cancer targeting and treatment strategy to utilize intracellular nonlethal enzymes through a combination of selective cancer stem-like cell (CSC) labeling and Click chemistry-mediated drug delivery. A de novo designed compound, AAMCHO [N-(3,4,6-triacetyl- N-azidoacetylmannosamine)-cis-2-ethyl-3-formylacrylamideglycoside], selectively labeled cancer CSCs in vitro and in vivo through enzymatic oxidation by intracellular aldehyde dehydrogenase 1A1. Notably, azide labeling is more efficient in identifying tumorigenic cell populations than endogenous markers such as CD44. A dibenzocyclooctyne (DBCO)-toxin conjugate, DBCO-MMAE (Monomethylauristatin E), could next target the labeled CSCs in vivo via bioorthogonal Click reaction to achieve excellent anticancer efficacy against a series of tumor models, including orthotopic xenograft, drug-resistant tumor, and lung metastasis with low toxicity. A 5/7 complete remission was observed after single-cycle treatment of an advanced triple-negative breast cancer xenograft (~500 mm3).

Tailoring Synthetic Polypeptide Design for Directed Fibril Superstructure Formation and Enhanced Hydrogel Properties.

The biological significance of self-assembled protein filament networks and their unique mechanical properties have sparked interest in the development of synthetic filament networks that mimic these attributes. Building on the recent advancement of autoaccelerated ring-opening polymerization of amino acid N-carboxyanhydrides (NCAs), this study strategically explores a series of random copolymers comprising multiple amino acids, aiming to elucidate the core principles governing gelation pathways of these purpose-designed copolypeptides. Utilizing glutamate (Glu) as the primary component of copolypeptides, two targeted pathways were pursued: first, achieving a fast fibrillation rate with lower interaction potential using serine (Ser) as a comonomer, facilitating the creation of homogeneous fibril networks; and second, creating more rigid networks of fibril clusters by incorporating alanine (Ala) and valine (Val) as comonomers. The selection of amino acids played a pivotal role in steering both the morphology of fibril superstructures and their assembly kinetics, subsequently determining their potential to form sample-spanning networks. Importantly, the viscoelastic properties of the resulting supramolecular hydrogels can be tailored according to the specific copolypeptide composition through modulations in filament densities and lengths. The findings enhance our understanding of directed self-assembly in high molecular weight synthetic copolypeptides, offering valuable insights for the development of synthetic fibrous networks and biomimetic supramolecular materials with custom-designed properties.

Mesoporous polydopamine Targeting CDK4/6 Inhibitor toward Brilliant Synergistic Immunotherapy of Breast Cancer.

Immunotherapy utilizing anti-PD-L1 blockade has achieved dramatic success in clinical breast cancer management but is often hampered by the limited immune response. Increasing evidence shows that immunogenic cell death (ICD) recently arises as a promising strategy for enlarging tumor immunogenicity and eliciting systemic anti-tumor immunity effectively. However, developing simple but versatile, highly efficient but low-toxic, biosafe, and clinically available transformed ICD inducers remains a huge demand and is highly desirable. Herein, a multifunctional ICD inducer is purposefully developed A6-MPDA@PAL by integrating photothermal therapy (PTT) nanoplatforms mesoporous polydopamine (MPDA), CDK4/6 inhibitor palbociclib (PAL), and CD44-specific targeting A6 peptide in a simple way for augmenting the immune antitumor efficacy of anti-PD-L1 therapy. Remarkably, the light-inducible nanoplatforms exhibit multiple favorable therapeutic features ensuring a superior and biosafe PTT/chemotherapy efficacy. Together with stronger accumulative ICD induction, single administration of A6-MPDA@PAL can trigger robust systemic antitumor immunity and abscopal effect with the assistance of anti-PD-L1 blockade by fascinating the intratumoral infiltration of T lymphocytes and reversing the immunosuppressive tumor microenvironment simultaneously, therapy achieving brilliant synergistic immunotherapy with effective tumor ablation. This study presents a simple and smart ICD inducer opening up attractive clinical possibilities for reinforcing the anti-PD-L1 therapy against breast cancer.

A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2.

The ideal vaccine against viruses such as influenza and SARS-CoV-2 must provide a robust, durable and broad immune protection against multiple viral variants. However, antibody responses to current vaccines often lack robust cross-reactivity. Here we describe a polymeric Toll-like receptor 7 agonist nanoparticle (TLR7-NP) adjuvant, which enhances lymph node targeting, and leads to persistent activation of immune cells and broad immune responses. When mixed with alum-adsorbed antigens, this TLR7-NP adjuvant elicits cross-reactive antibodies for both dominant and subdominant epitopes and antigen-specific CD8+ T-cell responses in mice. This TLR7-NP-adjuvanted influenza subunit vaccine successfully protects mice against viral challenge of a different strain. This strategy also enhances the antibody response to a SARS-CoV-2 subunit vaccine against multiple viral variants that have emerged. Moreover, this TLR7-NP augments antigen-specific responses in human tonsil organoids. Overall, we describe a nanoparticle adjuvant to improve immune responses to viral antigens, with promising implications for developing broadly protective vaccines.

2-Phenylcyclopropylmethylamine (PCPMA) as a privileged scaffold for central nervous system drug design.

The use of privileged scaffolds in medicinal chemistry is an effective way to accelerate the drug discovery process, especially at the hit/lead optimization stage. 2-Phenylcyclopropylmethylamine (PCPMA) is a less commonly used chemical scaffold in medicinal chemistry, but many PCPMA-containing compounds exert therapeutic effects for various diseases, in particular central nervous system (CNS) diseases such as depression, schizophrenia, sleep disorder, and Parkinson's disease. The backbone of the PCPMA scaffold enables a unique structure of an amino group linked to a benzene ring through an alkyl linker, making it a useful template for the design of bioactive compounds especially for CNS drug targets including aminergic GPCRs and transporters. This review summarizes the medicinal chemistry studies of PCPMA-containing drugs and drug-like molecules, their mechanisms of action, and biological activities. We conclude that PCPMA is a unique and useful privileged scaffold for CNS drug design.

Effect of different salts on the foaming properties of model protein systems for infant formula.

This multiscale study aimed to evaluate the effects of different salts (NaCl, KCl, MgCl2, and CaCl2) on the foaming capacity (FC) and foam stability (FS) of model protein systems (MPS) for infant formula via changes in surface and structural properties. Our results showed that the FC and FS of MPS were increased with the addition of NaCl, KCl, and MgCl2, whereas CaCl2 significantly decreased FC (79.5 ± 10.6%) and increased FS (93.2 ± 2.2%). The surface hydrophobicity was increased and the net charge and surface tension were reduced after the addition of salts. Structural analysis revealed the reduction of intensity of intrinsic fluorescence spectroscopy and UV absorption, and the conversion of α-helix into ß-strand, which was attributed to protein agglomeration. Additionally, MgCl2 and CaCl2 exhibited larger size and lower net charge compared with NaCl and KCl, indicating a greater ability to bind to charged amino acids and form larger aggregates. Correlation analysis indicated that FC was positively related to adsorbed protein and ß-turn and negatively correlated with particle size. In addition, FS showed a positive correlation with ß-strand, apparent viscosity, and zeta potential. However, it exhibited a negative correlation with ß-turn, α-helix, and sulfhydryl content. These results provide a theoretical reference for further understanding of the effect of salts on the foaming properties of MPS.

Comparison of lipidome profiles in human milk from Chinese Han and Korean ethnic groups based on high-throughput lipidomic techniques.

The composition of milk lipids varies across different ethnic sources. The lipidome profiles of Chinese Han human milk (HHM) and Chinese Korean human milk (KHM) were investigated in this study. A total of 741 lipids were identified in HHM and KHM. Twenty-eight differentially expressed lipids (DEL) were screened between the 2 milk groups; among these, 6 triacylglycerols (TG), 13 diacylglycerols (DG), 7 free fatty acids (FFA), and 1 monoglyceride (MG) were upregulated in KHM. Carnitine (CAR) was upregulated in HHM. Most DEL showed a single peak distribution in both groups. The correlations, related pathways and diseases of these DEL were further analyzed. The results demonstrated that DG, MG, and FFA showed highly positive correlations with each other (r > 0.8). The most enriched Kyoto Encyclopedia of Genes and Genomes (https://www.kegg.jp/kegg/) and Human Metabolome Database (http://www.hmdb.ca) pathways were inositol phosphate metabolism, and α-linolenic acid and linolenic acid metabolism, respectively. Major depressive disorder-related FFA (20:5) and FFA (22:6) were more abundant in KHM, whereas HHM showed more obesity-related CAR. These data potentially provide lipidome information regarding human milk from different ethnicities in China.

Adenosine A2A Receptor (A2AAR) Ligand Screening Using the 19F-NMR Probe FPPA.

The binding affinity of G protein-coupled receptor (GPCR) ligands is customarily measured by radio-ligand competition experiments. As an alternative approach, 19F nuclear magnetic resonance spectroscopy (19F-NMR) is used for the screening of small-molecule lead compounds in drug discovery; the two methods are complementary in that the measurements are performed with widely different experimental conditions. Here, we used the structure of the A2A adenosine receptor (A2AAR) complex with V-2006 (3-(4-amino-3-methylbenzyl)-7-(furan-2-yl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine) as the basis for the design of a fluorine-containing probe molecule, FPPA (4-(furan-2-yl)-7-(4-(trifluoromethyl)benzyl)-7H-pyrrolo[2,3-d]pyramidin-2-amine), for binding studies with A2AAR. A protocol of experimental conditions for drug screening and measurements of drug binding affinities using 1D 19F-NMR observation of FPPA is validated with studies of known A2AAR ligands. 19F-NMR with FPPA is thus found to be a robust approach for the discovery of ligands with new core structures, which will expand the libraries of A2AAR-targeting drug candidates.

A review on polyphenols and their potential application to reduce food allergenicity.

This review summarized recent studies about the effects of polyphenols on the allergenicity of allergenic proteins, involving epigallocatechin gallate (EGCG), caffeic acid, chlorogenic acid, proanthocyanidins, quercetin, ferulic acid and rosmarinic acid, etc. Besides, the mechanism of polyphenols for reducing allergenicity was discussed and concluded. It was found that polyphenols could noncovalently (mainly hydrophobic interactions and hydrogen bonding) and covalently (mainly alkaline, free-radical grafting, and enzymatic method) react with allergens to induce the structural changes, resulting in the masking or/and destruction of epitopes and the reduction of allergenicity. Oral administration in murine models showed that the allergic reaction might be suppressed by regulating immune cell function, changing the levels of cytokines, suppressing of MAPK, NF-κb and allergens-presentation pathway and improving intestine function, etc. The outcome of reduced allergenicity and suppressed allergic reaction was affected by many factors such as polyphenol types, polyphenol concentration, allergen types, pH, oral timing and dosage. Moreover, the physicochemical and functional properties of allergenic proteins were improved after treatment with polyphenols. Therefore, polyphenols have the potential to produce hypoallergenic food. Further studies should focus on active concentrations and bioavailability of polyphenols, confirming optimal intake and hypoallergenic of polyphenols based on clinical trials.

Effect of high hydrostatic pressure on the edible quality, health and safety attributes of plant-based foods represented by cereals and legumes: a review.

Consumers today are increasingly willing to reduce their meat consumption and adopt plant-based alternatives in their diet. As a main source of plant-based foods, cereals and legumes (CLs) together could make up for all the essential nutrients that humans consume daily. However, the consumption of CLs and their derivatives is facing many challenges, such as the poor palatability of coarse grains and vegetarian meat, the presence of anti-nutritional factors, and allergenic proteins in CLs, and the vulnerability of plant-based foods to microbial contamination. Recently, high hydrostatic pressure (HHP) technology has been used to tailor the techno-functionality of plant proteins and induce cold gelatinization of starch in CLs to improve the edible quality of plant-based products. The nutritional value (e.g., the bioavailability of vitamins and minerals, reduction of anti-nutritional factors of legume proteins) and bio-functional properties (e.g., production of bioactive peptides, increasing the content of γ-aminobutyric acid) of CLs were significantly improved as affected by HHP. Moreover, the food safety of plant-based products could be significantly improved as well. HHP lowered the risk of microbial contamination through the inactivation of numerous microorganisms, spores, and enzymes in CLs and alleviated the allergy symptoms from consumption of plant-based foods.

Proteomic characterization and comparison of milk fat globule membrane proteins of Saanen goat milk from 3 habitats in China using SWATH-MS technique.

Saanen goats are among the major dairy goats in China. In present study, variation of milk fat globule membrane proteins profile of Saanen goat milk caused by geographic location was investigated using sequential window acquisition of all theoretical fragment ions data-independent acquisition mass spectrometry based proteomic approach. A total of 1,001 proteins were quantified in goat milk collected from 3 habitats of China [Guangdong (GD); Inner Mongolia (IM); Shannxi (SX)]. Most of the proteins were found to act cellular process of biological process, cell of cellular component, binding of molecular function after Gene Ontology annotation and metabolic of pathway indicated by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Differentially expressed proteins (DEP) for GD versus IM, GD versus SX, IM versus SX were identified to be 81, 91, and 44, respectively. Gene Ontology enrichment analysis showed that the greatest DEP for 3 groups (GD vs. IM, GD vs. SX, IM vs. SX) were cellular process, cellular process and organonitrogen compound biosynthetic process/immune system process for biological process. For cellular component, the largest number of DEP for 3 comparison groups were organelle, organelle and organelle/intracellular. For molecular function, DEP of the 3 comparison groups were expressed most in structural molecule activity, binding and anion binding, respectively. Pathways with the majority of DEP were ribosome, systemic lupus erythematosus and primary immunodeficiency/systemic lupus erythematosus/amoebiasis/PI3K-Akt signaling pathway for GD versus IM, GD versus SX and IM versus SX, severally. Protein-protein interaction network analysis showed that DEP interacted most were 40S ribosomal protein S5, fibronectin and Cytochrome b-c1 complex subunit 2, mitochondrial for GD versus IM, GD versus SX and IM versus SX, separately. Data may give useful information for goat milk selection and milk authenticity in China.

Modeling and Designing Particle-Regulated Amyloid-like Assembly of Synthetic Polypeptides in Aqueous Solution.

In cells, actin and tubulin polymerization is regulated by nucleation factors, which promote the nucleation and subsequent growth of protein filaments in a controlled manner. Mimicking this natural mechanism to control the supramolecular polymerization of macromolecular monomers by artificially created nucleation factors remains a largely unmet challenge. Biological nucleation factors act as molecular scaffolds to boost the local concentrations of protein monomers and facilitate the required conformational changes to accelerate the nucleation and subsequent polymerization. An accelerated assembly of synthetic poly(l-glutamic acid) into amyloid fibrils catalyzed by cationic silica nanoparticle clusters (NPCs) as artificial nucleation factors is demonstrated here and modeled as supramolecular polymerization with a surface-induced heterogeneous nucleation pathway. Kinetic studies of fibril growth coupled with mechanistic analysis demonstrate that the artificial nucleators predictably accelerate the supramolecular polymerization process by orders of magnitude (e.g., shortening the assembly time by more than 10 times) when compared to the uncatalyzed reaction, under otherwise identical conditions. Amyloid-like fibrillation was supported by a variety of standard characterization methods. Nucleation followed a Michaelis-Menten-like scheme for the cationic silica NPCs, while the corresponding anionic or neutral nanoparticles had no effect on fibrillation. This approach shows the effectiveness of charge-charge interactions and surface functionalities in facilitating the conformational change of macromolecular monomers and controlling the rates of nucleation for fibril growth. Molecular design approaches like these inspire the development of novel materials via biomimetic supramolecular polymerizations.

Recent advances in alleviating food allergenicity through fermentation.

The increasing prevalence of food allergies is a significant challenge to global food health and safety. Various strategies have been deployed to decrease the allergenicity of food for preventing and reducing related disorders. Compared to other methods, fermentation has unique advantages in reducing the allergenicity of food and may represent a new trend in preventing food-induced allergies. This review introduces the characteristics of allergens in various foods, including shellfish, soy, peanut, milk, tree nut, egg, wheat, and fish. The mechanism and pathological symptoms of allergic reactions are then summarized. Furthermore, the advantages of fermentation for reducing the allergenicity of these foods and preventing allergies are evaluated. Fermentation is an efficient approach for reducing or eliminating food allergenicity. Simultaneously, it improved the nutritional value and physicochemical properties of food materials. It is conceivable that a combination of mixed strain fermentation with additional processing, such as heat treatment, pulsed light, and ultrasonication, will efficiently reduce the allergenicity of various foods and preserve their unique taste and nutritional components, providing significance for patients with allergies.

Food irradiation: a promising technology to produce hypoallergenic food with high quality.

The increasing incidence of food allergy cases is a public health problem of global concern. Producing hypoallergenic foods with high quality, low cost, and eco-friendly is a new trend for the food industry in the coming decades. Food irradiation, a non-thermal food processing technology, is a powerful tool to reduce the allergenicity with the above advantages. This review presents a summary of recent studies about food irradiation to reduce the allergenicity of food, including shellfish, soy, peanut, milk, tree nut, egg, wheat and fish. Principles of food irradiation, including mechanisms of allergenicity-reduction, irradiation types and characteristics, are discussed. Specific effects of food irradiation are also evaluated, involving microbial decontamination, improvement or preservation of nutritional value, harmful substances reduction of food products. Furthermore, the advantages, disadvantages and limitations of food irradiation are analyzed. It is concluded that food irradiation is a safety tool to reduce the allergenicity of food effectively, with high nutritional value and long shelf-life, making it a competitive alternative technology to traditional techniques such as heating treatments. Of note, a combination of irradiation with additional processing may be a trend for food irradiation.

Bioresorbable silicon electronic sensors for the brain.

Many procedures in modern clinical medicine rely on the use of electronic implants in treating conditions that range from acute coronary events to traumatic injury. However, standard permanent electronic hardware acts as a nidus for infection: bacteria form biofilms along percutaneous wires, or seed haematogenously, with the potential to migrate within the body and to provoke immune-mediated pathological tissue reactions. The associated surgical retrieval procedures, meanwhile, subject patients to the distress associated with re-operation and expose them to additional complications. Here, we report materials, device architectures, integration strategies, and in vivo demonstrations in rats of implantable, multifunctional silicon sensors for the brain, for which all of the constituent materials naturally resorb via hydrolysis and/or metabolic action, eliminating the need for extraction. Continuous monitoring of intracranial pressure and temperature illustrates functionality essential to the treatment of traumatic brain injury; the measurement performance of our resorbable devices compares favourably with that of non-resorbable clinical standards. In our experiments, insulated percutaneous wires connect to an externally mounted, miniaturized wireless potentiostat for data transmission. In a separate set-up, we connect a sensor to an implanted (but only partially resorbable) data-communication system, proving the principle that there is no need for any percutaneous wiring. The devices can be adapted to sense fluid flow, motion, pH or thermal characteristics, in formats that are compatible with the body's abdomen and extremities, as well as the deep brain, suggesting that the sensors might meet many needs in clinical medicine.

Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides.

Ribozymes synthesize proteins in a highly regulated local environment to minimize side reactions caused by various competing species. In contrast, it is challenging to prepare synthetic polypeptides from the polymerization of N-carboxyanhydrides (NCAs) in the presence of water and impurities, which induce monomer degradations and chain terminations, respectively. Inspired by natural protein synthesis, we herein report the preparation of well-defined polypeptides in the presence of competing species, by using a water/dichloromethane biphasic system with macroinitiators anchored at the interface. The impurities are extracted into the aqueous phase in situ, and the localized macroinitiators allow for NCA polymerization at a rate which outpaces water-induced side reactions. Our polymerization strategy streamlines the process from amino acids toward high molecular weight polypeptides with low dispersity by circumventing the tedious NCA purification and the demands for air-free conditions, enabling low-cost, large-scale production of polypeptides that has potential to change the paradigm of polypeptide-based biomaterials.

Comparative analysis of caseins in Saanen goat milk from 3 different regions of China using quantitative proteomics.

A quantitative proteomic technique based on data-independent acquisition (DIA) was used to analyze differentially expressed caseins of Saanen goat milk samples collected from 3 regions in China (Guangdong, GD; Inner Mongolia, IM; Shaanxi, SX). A total of 345 proteins were quantified in each sample. Gene Ontology (GO) analysis showed that proteins were mainly involved in cellular process and cell and binding functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that proteins were mainly involved in metabolic pathways. Differentially expressed proteins (DEP) between goat milk from 3 comparison groups composed of paired regions were compared and analyzed. The number of DEP was 114, 69, and 79 for GD versus IM, GD versus SX, and IM versus SX, respectively. The GO enrichment analysis of the 3 comparison groups showed that differences were mainly related to the regulation of biological quality, biological regulation, and response to stimulus in terms of biological process; extracellular region for cellular component; and binding function for molecular function. Pathways in which DEP of GD versus IM, GD versus SX, and IM versus SX were mostly protein processing in endoplasmic reticulum for the first 2 groups and metabolic pathways for the last. Protein-protein interaction network analysis demonstrated that the most prominent DEP was heat shock protein 90 ß family member 1 for both the GD versus IM and the GD versus SX groups, and haptoglobin for the IM versus SX group. Data from this study may offer useful information for further investigation of the protein composition of Saanen goat milk and its application in the dairy industry.