# Vildagliptin and Omarigliptin Differentially Bind to DPP‐4 Homodimers and Modulate Osteoclast‐Mediated Bone Resorption

**Authors:** Ratchaneevan Aeimlapa, Jiraporn Panmanee, Jarinthorn Teerapornpuntakit, Kannikar Wongdee, Jirawan Thongbunchoo, Nattapon Panupinthu, Saovaros Svasti, Nattayaporn Apaijai, Piangkwan Sa‐nguanmoo, Siriporn Chattipakorn, Nipon Chattipakorn, Narattaphol Charoenphandhu

PMC · DOI: 10.1002/cph4.70103 · 2026-01-21

## TL;DR

This study shows that two DPP-4 inhibitors, vildagliptin and omarigliptin, affect bone health differently in diabetic rats, with omarigliptin being more effective at reducing bone resorption.

## Contribution

The study reveals the distinct mechanisms by which vildagliptin and omarigliptin modulate bone resorption through their differential binding to DPP-4 homodimers.

## Key findings

- Vildagliptin improved bone microstructure but did not reduce osteoclast activity in rats.
- Omarigliptin reduced osteoclast numbers and inhibited key osteoclast genes, suggesting better anti-resorptive effects.
- Molecular simulations showed omarigliptin binds more tightly to DPP-4 homodimers, possibly explaining its greater efficacy.

## Abstract

Increased fracture risk in prediabetes and diabetes mellitus partly arises from bone collagen damage and enhanced bone resorption. Certain antidiabetic agents—particularly thiazolidinediones—paradoxically aggravate bone loss and fractures, especially in postmenopausal women with osteoporosis. However, dipeptidyl peptidase‐4 (DPP‐4) inhibitors (e.g., vildagliptin and omarigliptin) might help prevent diabetic osteopathy, although variable outcomes have been observed due to unknown mechanisms. Herein, we used high‐fat diet‐fed rats to demonstrate that oral administration of vildagliptin for 4 weeks not only alleviated insulin resistance but also improved tibial bone microstructure, as determined by bone histomorphometry. Further in vitro investigations in primary osteoblasts showed that both vildagliptin and omarigliptin similarly increased osteoblast viability, rather than upregulating the expression of osteoblast‐specific genes (e.g., Runx2 and alkaline phosphatase). We also used primary multinucleated osteoclasts to elucidate how the two DPP‐4 inhibitors modulated osteoclast functions. Interestingly, only omarigliptin, but not vildagliptin, reduced the number of TRAP‐positive cells and the mRNA expression of osteoclast‐specific genes (e.g., RANK and cathepsin K). In silico molecular dynamics revealed that omarigliptin and vildagliptin interacted differently with the DPP‐4 homodimer. Transient binding to one chain and tight binding to the other chain of the DPP‐4 homodimer by omarigliptin may be associated with its higher potency in inhibiting bone resorption. In conclusion, DPP‐4 inhibitors could improve bone microstructure, in part by increasing osteoblast viability and inhibiting osteoclast‐mediated bone resorption. Thus, omarigliptin may offer greater benefits to diabetic patients with osteoporosis, as it also helps suppress osteoclastogenesis and bone resorption.

Vildagliptin and omarigliptin, dipeptidyl peptidase‐4 (DPP‐4) inhibitors, have differential effects on bone cells. Although vildagliptin improved the bone microstructure of high‐fat diet‐fed rats, it was unable to downregulate osteoclastogenesis or the expression of key osteoclast transcripts. Conversely, omarigliptin effectively attenuated bone resorption by suppressing osteoclast differentiation, maturation, and resorptive activity.

## Linked entities

- **Genes:** RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860], TNFRSF11A (TNF receptor superfamily member 11a) [NCBI Gene 8792]
- **Proteins:** DPP4 (dipeptidyl peptidase 4)
- **Chemicals:** vildagliptin (PubChem CID 6918537), omarigliptin (PubChem CID 46209133)
- **Diseases:** prediabetes (MONDO:0006920), diabetes mellitus (MONDO:0005015), osteoporosis (MONDO:0005298)
- **Species:** Rattus norvegicus (taxon 10116)

## Full-text entities

- **Genes:** CTSK (cathepsin K) [NCBI Gene 1513] {aka CTS02, CTSO, CTSO1, CTSO2, PKND, PYCD}, Vip (vasoactive intestinal polypeptide) [NCBI Gene 22353], alp (alopecia, recessive) [NCBI Gene 11691], INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, Atp6v0d2 (ATPase, H+ transporting, lysosomal V0 subunit D2) [NCBI Gene 242341] {aka 1620401A02Rik, V-ATPase}, Acp5 (acid phosphatase 5, tartrate resistant) [NCBI Gene 11433] {aka TRACP, TRAP}, Igf1 (insulin-like growth factor 1) [NCBI Gene 16000] {aka C730016P09Rik, Igf-1, Igf-I}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Dpp4 (dipeptidylpeptidase 4) [NCBI Gene 25253] {aka CD26, DPPIV}, DPP4 (dipeptidyl peptidase 4) [NCBI Gene 1803] {aka ADABP, ADCP2, CD26, DPPIV, TP103}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}, Gip (gastric inhibitory polypeptide) [NCBI Gene 14607], CD86 (CD86 molecule) [NCBI Gene 942] {aka B7-2, B7.2, B70, BU63, CD28LG2, CD86 v6}, Itgav (integrin alpha V) [NCBI Gene 16410] {aka 1110004F14Rik, 2610028E01Rik, CD51, D430040G12Rik}, Gcg (glucagon) [NCBI Gene 14526] {aka GLP-1, Glu, PPG}, Fos (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 14281] {aka D12Rfj1, c-fos, cFos}, TNFSF11 (TNF superfamily member 11) [NCBI Gene 8600] {aka CD254, ODF, OPGL, OPTB2, RANKL, TNLG6B}, DSPP (dentin sialophosphoprotein) [NCBI Gene 1834] {aka DFNA39, DGI1, DMP3, DPP, DSP}, GIP (gastric inhibitory polypeptide) [NCBI Gene 2695], Bcl2 (B cell leukemia/lymphoma 2) [NCBI Gene 12043] {aka Bcl-2, C430015F12Rik, D630044D05Rik, D830018M01Rik}, TRAP [NCBI Gene 100187907], Cdkn2a (cyclin dependent kinase inhibitor 2A) [NCBI Gene 12578] {aka ARF-INK4a, Arf, INK4a-ARF, Ink4a/Arf, MTS1, Pctr1}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, MAPK14 (mitogen-activated protein kinase 14) [NCBI Gene 1432] {aka CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2}, CAV1 (caveolin 1) [NCBI Gene 857] {aka BSCL3, CGL3, LCCNS, MSTP085, PPH3, VIP21}, Itgb3 (integrin beta 3) [NCBI Gene 16416] {aka CD61, GP3A, INGRB3}, Lif (leukemia inhibitory factor) [NCBI Gene 16878], Runx2 (runt related transcription factor 2) [NCBI Gene 12393] {aka AML3, CBF-alpha-1, Cbf, Cbfa-1, Cbfa1, LS3}, Bglap2 (bone gamma-carboxyglutamate protein 2) [NCBI Gene 12097] {aka BGP2, Bglap1, Bgp, Og2, mOC-B}, Csf1 (colony stimulating factor 1 (macrophage)) [NCBI Gene 12977] {aka BAP025, Csfm, MCSF, Mhdabap25, PG-M-CSF, op}, Npy (neuropeptide Y) [NCBI Gene 109648] {aka 0710005A05Rik}, SLC5A2 (solute carrier family 5 member 2) [NCBI Gene 6524] {aka SGLT2}, RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860] {aka AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD}, Calcr (calcitonin receptor) [NCBI Gene 12311] {aka Clr, Ct-r}, GLP1R (glucagon like peptide 1 receptor) [NCBI Gene 2740] {aka GLP-1, GLP-1-R, GLP-1R}, Cst3 (cystatin C) [NCBI Gene 13010] {aka CysC}, Cdkn1a (cyclin dependent kinase inhibitor 1A) [NCBI Gene 12575] {aka CAP20, CDKI, CIP1, Cdkn1, P21, SDI1}, Nfatc1 (nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1) [NCBI Gene 18018] {aka 2210017P03Rik, NF-ATc, NFAT2, NFATc, Nfatcb}, Ccnd1 (cyclin D1) [NCBI Gene 12443] {aka CycD1, Cyl-1, PRAD1, bcl-1, cD1}, Tac1 (tachykinin 1) [NCBI Gene 21333] {aka 4930528L02Rik, NK-1, NK1, Nkna, PPT-A, PPTA}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, NPY (neuropeptide Y) [NCBI Gene 4852] {aka PYY4}, Tnfsf11 (tumor necrosis factor (ligand) superfamily, member 11) [NCBI Gene 21943] {aka Ly109l, ODF, OPGL, RANKL, Trance}, Dpp4 (dipeptidylpeptidase 4) [NCBI Gene 13482] {aka Cd26, Dpp-4, THAM}
- **Diseases:** fragility fractures (MESH:D005600), calcium (MESH:D002128), CTX (MESH:D019294), prediabetes (MESH:D011236), bone defects (MESH:D001847), DM (MESH:D003920), insulin resistance (MESH:D007333), T1DM (MESH:D003922), inflammatory (MESH:D007249), metabolic disorder (MESH:D008659), bone fractures (MESH:D050723), dyslipidemia (MESH:D050171), collagen (MESH:D003095), multiple myeloma (MESH:D009101), osteosarcoma (MESH:D012516), hyperlipidemia (MESH:D006949), obesity (MESH:D009765), bone fragility (MESH:C536063), adenocarcinoma (MESH:D000230), low bone (MESH:D001851), hypoglycemia (MESH:D007003), osteoporosis (MESH:D010024), ND (MESH:C537849), T2DM (MESH:D003924)
- **Chemicals:** dl-methionine (MESH:D064697), oxygen (MESH:D010100), alpha-MEM (MESH:C420642), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MESH:C022616), anagliptin (MESH:C583175), TG (MESH:D013866), Linagliptin (MESH:D000069476), zolazepam (MESH:D015041), Omarigliptin (MESH:C587539), penicillin (MESH:D010406), carbon (MESH:D002244), ascorbate-2-phosphate (MESH:C011669), Nonidet P-40 (MESH:C010615), paraformaldehyde (MESH:C003043), polystyrene (MESH:D011137), TC (MESH:D013667), streptomycin (MESH:D013307), ethanol (MESH:D000431), triglyceride (MESH:D014280), Trelagliptin (MESH:C000595449), tungsten carbide (MESH:C002802), NaCl (MESH:D012965), LPS (MESH:D008070), water (MESH:D014867), CO2 (MESH:D002245), xylazine (MESH:D014991), cholesterol (MESH:D002784), blood glucose (MESH:D001786), HCl (MESH:D006851), sodium borate (MESH:C010634), glucose (MESH:D005947), fluoride (MESH:D005459), ammonium hydroxide (MESH:D064753), 4',6-diamidino-2-phenylindole (MESH:C007293), Pi (MESH:D010716), toluidine blue (MESH:D014048), saxagliptin (MESH:C502994), calcium (MESH:D002118), methyl methacrylate (MESH:D020366), lard (MESH:C029310), TRIzol (MESH:C411644), lipid (MESH:D008055), Vildagliptin (MESH:D000077597), nitrogen (MESH:D009584), formalin (MESH:D005557), canagliflozin (MESH:D000068896), pioglitazone (MESH:D000077205), sulfur (MESH:D013455), tiletamine (MESH:D013992), thiazolidinediones (MESH:D045162), fat (MESH:D005223), phosphorus (MESH:D010758), Cl- (MESH:D002713), isopropanol (MESH:D019840), DMEM (-), Sitagliptin (MESH:D000068900), Na+ (MESH:D012964)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** C-23 C, C-60 C
- **Cell lines:** PMC-AK04F-COS — Homo sapiens (Human), Astrocytoma, Cancer cell line (CVCL_1093), MC3T3-E1 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0409), /6 — Homo sapiens (Human), Tongue squamous cell carcinoma, Cancer cell line (CVCL_5985), TEC — Scophthalmus maximus (Turbot), Spontaneously immortalized cell line (CVCL_J026), 462 — Homo sapiens (Human), Lung small cell carcinoma, Cancer cell line (CVCL_A567)

## Figures

11 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12824438/full.md

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Source: https://tomesphere.com/paper/PMC12824438