Target type: biologicalprocess
The process of creating a trabecula in the bone. A trabecula is a tissue element in the form of a small beam, strut or rod. [GOC:dph]
Bone trabecula formation, a complex process essential for skeletal strength and bone marrow support, involves a coordinated interplay of cellular and molecular events. It begins with the differentiation of mesenchymal stem cells into osteoblasts, the cells responsible for bone matrix synthesis. Osteoblasts deposit an organic matrix composed primarily of type I collagen and other proteins, which is subsequently mineralized with calcium phosphate crystals. This process, known as osteogenesis, results in the formation of thin, interconnected plates of bone known as trabeculae. The formation of trabeculae is influenced by various factors, including mechanical loading, hormonal signaling, and growth factors. As trabeculae develop, they undergo a process of remodeling, involving bone resorption by osteoclasts, specialized cells that degrade bone tissue, and subsequent bone formation by osteoblasts. This dynamic balance between bone formation and resorption ensures the maintenance of bone mass and the adaptation of trabecular architecture to changing mechanical demands. The formation of trabeculae is highly regulated by a complex network of signaling pathways, including the Wnt, BMP, and RANKL/RANK/OPG pathways. These pathways control the differentiation and function of osteoblasts and osteoclasts, thereby regulating the rate and direction of bone remodeling. Trabecular formation is crucial for maintaining bone strength and supporting bone marrow function. Defects in trabecula formation can lead to bone diseases such as osteoporosis, characterized by decreased bone mass and increased fracture risk. Understanding the intricate mechanisms of trabecula formation is essential for developing effective therapies for bone diseases and promoting bone health.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| Secreted frizzled-related protein 1 | A secreted frizzled-related protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8N474] | Homo sapiens (human) |
| Vascular endothelial growth factor A | A vascular endothelial growth factor A, long form that is encoded in the genome of human. [PRO:DNx, UniProtKB:P15692] | Homo sapiens (human) |
| 72 kDa type IV collagenase | A 72 kDa type IV collagenase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P08253] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| 2,3-dihydroxybenzoic acid | 2,3-dihydroxybenzoic acid : A dihydroxybenzoic acid that is benzoic acid substituted by hydroxy groups at positions 2 and 3. It occurs naturally in Phyllanthus acidus and in the aquatic fern Salvinia molesta. 2,3-dihydroxybenzoic acid: RN given refers to parent cpd dihydroxybenzoic acid : Any member of the class of hydroxybenzoic acids carrying two phenolic hydroxy groups on the benzene ring and its derivatives. | dihydroxybenzoic acid | human xenobiotic metabolite; plant metabolite |
| protocatechuic acid | 3,4-dihydroxybenzoic acid : A dihydroxybenzoic acid in which the hydroxy groups are located at positions 3 and 4. protocatechuic acid: RN given refers to parent cpd; structure | catechols; dihydroxybenzoic acid | antineoplastic agent; EC 1.1.1.25 (shikimate dehydrogenase) inhibitor; EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitor; human xenobiotic metabolite; plant metabolite |
| gallic acid | gallate : A trihydroxybenzoate that is the conjugate base of gallic acid. | trihydroxybenzoic acid | antineoplastic agent; antioxidant; apoptosis inducer; astringent; cyclooxygenase 2 inhibitor; EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitor; geroprotector; human xenobiotic metabolite; plant metabolite |
| beta-resorcylic acid | beta-resorcylic acid: RN given refers to parent cpd; structure | ||
| oxyquinoline | Oxyquinoline: An antiseptic with mild fungistatic, bacteriostatic, anthelmintic, and amebicidal action. It is also used as a reagent and metal chelator, as a carrier for radio-indium for diagnostic purposes, and its halogenated derivatives are used in addition as topical anti-infective agents and oral antiamebics. quinolin-8-ol : A monohydroxyquinoline that is quinoline substituted by a hydroxy group at position 8. Its fungicidal properties are used for the control of grey mould on vines and tomatoes. | monohydroxyquinoline | antibacterial agent; antifungal agrochemical; antiseptic drug; iron chelator |
| acetohydroxamic acid | acetohydroxamic acid : A member of the class of acetohydroxamic acids that is acetamide in which one of the amino hydrogens has been replaced by a hydroxy group. acetohydroxamic acid: urease inhibitor N-hydroxyacetimidic acid : A carbohydroximic acid consisting of acetimidic acid having a hydroxy group attached to the imide nitrogen. oxime : Compounds of structure R2C=NOH derived from condensation of aldehydes or ketones with hydroxylamine. Oximes from aldehydes may be called aldoximes; those from ketones may be called ketoximes. | acetohydroxamic acids; carbohydroximic acid | algal metabolite; EC 3.5.1.5 (urease) inhibitor |
| 2,5-dihydroxybenzoic acid | 2,5-dihydroxybenzoic acid : A dihydroxybenzoic acid having the two hydroxy groups at the 2- and 5-positions. 2,5-dihydroxybenzoic acid: RN given refers to parent cpd; a oxidative product of saligenin | dihydroxybenzoic acid | EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitor; fungal metabolite; human metabolite; MALDI matrix material; mouse metabolite |
| nafamostat | nafamostat: inhibitor of trypsin, plasmin, pancreatic kallikrein, plasma kallikrein & thrombin; strongly inhibits esterolytic activities of C1r & C1 esterase complement-mediated hemolysis; antineoplastic | benzoic acids; guanidines | |
| 4-phenylphenol | 4-phenylphenol: RN given refers to cpd without isomeric designation biphenyl-4-ol : A member of the class of hydroxybiphenyls that is biphenyl carrying a hydroxy group at position 4. | hydroxybiphenyls | |
| veratric acid | 3,4-dimethoxybenzoic acid : A member of the class of benzoic acids that is benzoic acid substituted by methoxy groups at positions 2 and 3. veratric acid: RN given refers to parent cpd; structure | benzoic acids | allergen; plant metabolite |
| methyl gallate | methyl 3,4,5-trihydroxybenzoate : A gallate ester obtained by the formal condensation of gallic acid with methanol. It exhibits anti-oxidant, anti-tumor, anti-microbial and anti-inflammatory properties. methyl gallate: has both immunosuppressive and phytogenic antineoplastic activities; isolated from Acer saccharinum | gallate ester | anti-inflammatory agent; antioxidant; plant metabolite |
| 3,4,5-trimethoxybenzoic acid | 3,4,5-trimethoxybenzoic acid : A benzoic acid derivative carrying 3-, 4- and 5-methoxy substituents. 3,4,5-trimethoxybenzoic acid: RN given refers to parent cpd; structure | benzoic acids; methoxybenzenes | human urinary metabolite; human xenobiotic metabolite; plant metabolite |
| syringic acid | syringic acid : A dimethoxybenzene that is 3,5-dimethyl ether derivative of gallic acid. syringic acid: RN given refers to parent cpd; structure in third source | benzoic acids; dimethoxybenzene; phenols | plant metabolite |
| tropolone | tropolone : A cyclic ketone that is cyclohepta-2,4,6-trien-1-one substituted by a hydroxy group at position 2. It is a toxin produced by the agricultural pathogen Burkholderia plantarii. Tropolone: A seven-membered aromatic ring compound. It is structurally related to a number of naturally occurring antifungal compounds (ANTIFUNGAL AGENTS). | alpha-hydroxy ketone; cyclic ketone; enol | bacterial metabolite; fungicide; toxin |
| methylene diphosphonate | medronic acid : A 1,1-bis(phosphonic acid) consisting of methane substituted by two phosphonic acid groups. | 1,1-bis(phosphonic acid) | bone density conservation agent; chelator |
| clodronic acid | clodronic acid : An organochlorine compound that is methylene chloride in which both hydrogens are replaced by phosphonic acid groups. It inhibits bone resorption and soft tissue calcification, and is used (often as the disodium salt tetrahydrate) as an adjunct in the treatment of severe hypercalcaemia associated with malignancy, and in the management of osteolytic lesions and bone pain associated with skeletal metastases. Clodronic Acid: A diphosphonate which affects calcium metabolism. It inhibits bone resorption and soft tissue calcification. | 1,1-bis(phosphonic acid); one-carbon compound; organochlorine compound | antineoplastic agent; bone density conservation agent |
| daunorubicin | anthracycline : Anthracyclines are polyketides that have a tetrahydronaphthacenedione ring structure attached by a glycosidic linkage to the amino sugar daunosamine. daunorubicin : A natural product found in Actinomadura roseola. Daunorubicin: A very toxic anthracycline aminoglycoside antineoplastic isolated from Streptomyces peucetius and others, used in treatment of LEUKEMIA and other NEOPLASMS. | aminoglycoside antibiotic; anthracycline; p-quinones; tetracenequinones | antineoplastic agent; bacterial metabolite |
| tiludronic acid | tiludronic acid: a bone resorption inhibitor; an antihypercalcemic agent; used in the tratment of Paget's disease; used in the treatment and prevention of osteoporosis; structure given in first source | organochlorine compound | |
| epigallocatechin gallate | (-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin. epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis) | flavans; gallate ester; polyphenol | antineoplastic agent; antioxidant; apoptosis inducer; geroprotector; Hsp90 inhibitor; neuroprotective agent; plant metabolite |
| 4-phenylbenzoic acid | 4-phenylbenzoic acid: RN given refers to 4-carboxylic cpd | ||
| zoledronic acid | zoledronic acid : An imidazole compound having a 2,2-bis(phosphono)-2-hydroxyethane-1-yl substituent at the 1-position. Zoledronic Acid: An imidobisphosphonate inhibitor of BONE RESORPTION that is used for the treatment of malignancy-related HYPERCALCEMIA; OSTEITIS DEFORMANS; and OSTEOPOROSIS. | 1,1-bis(phosphonic acid); imidazoles | bone density conservation agent |
| piloty's acid | Piloty's acid: structure in first source | sulfonamide | |
| ubenimex | ubenimex: growth inhibitor | ||
| 8-mercaptoquinoline | 8-mercaptoquinoline: structure given in first source | ||
| marimastat | marimastat : A secondary carboxamide resulting from the foraml condensation of the carboxy group of (2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoic acid with the alpha-amino group of N,3-dimethyl-L-valinamide. marimastat: a matrix metalloproteinase inhibitor active in patients with advanced carcinoma of the pancreas, prostate, or ovary | hydroxamic acid; secondary carboxamide | antineoplastic agent; matrix metalloproteinase inhibitor |
| n-(2-isobutyl-3-(n'-hydroxycarbonylamido)propanoyl)-o-methyltyrosinemethylamide | N-(2-isobutyl-3-(N'-hydroxycarbonylamido)propanoyl)-O-methyltyrosinemethylamide: RN given refers to the (S-(R*,S*))-isomer | ||
| ilomastat | CS 610: matrix metalloproteinase inhibitor; structure in first source ilomastat : An N-acyl-amino acid obtained by formal condensation of the carboxy group of (2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoic acid with the amino group of N-methyl-L-tryptophanamide. A cell permeable broad-spectrum matrix metalloproteinase (MMP) inhibitor | hydroxamic acid; L-tryptophan derivative; N-acyl-amino acid | anti-inflammatory agent; antibacterial agent; antineoplastic agent; EC 3.4.24.24 (gelatinase A) inhibitor; neuroprotective agent |
| bb3497 | BB3497: peptide deformylase inhibitor; structure in first source | ||
| procyanidin C1 | procyanidin C1 : A proanthocyanidin consisting of three (-)-epicatechin units joined by two successive (4beta->8)-linkages. procyanidin trimer C1: a flavonoid found in multiple plant sources including grape, apple, and cacao, which has antioxidant and anti-inflammatory properties | hydroxyflavan; polyphenol; proanthocyanidin | anti-inflammatory agent; antioxidant; EC 1.17.3.2 (xanthine oxidase) inhibitor; EC 3.2.1.20 (alpha-glucosidase) inhibitor; lipoxygenase inhibitor; metabolite |
| 3-((benzyl)(methylaminocarbonyl)methylaminocarbonyl)n-hydroxy-5-methylhexanamide | 3-((benzyl)(methylaminocarbonyl)methylaminocarbonyl)N-hydroxy-5-methylhexanamide: structure in first source | ||
| 2-(4-aminophenyl)benzothiazole | 2-(4-aminophenyl)benzothiazole: an agent with selective profile of in vitro anti-tumour activity; structure in first source | ||
| taxifolin | (+)-taxifolin : A taxifolin that has (2R,3R)-configuration. | taxifolin | metabolite |
| actinonin | actinonin: natural hydroxamic acid, pseudopeptide antibiotic isolated from Streptomyces species; structure | ||
| cgs 27023a | CGS 27023A: a matrix metalloproteinase inhibitor | ||
| aclarubicin | aclacinomycin A : An anthracycline antibiotic that is produced by Streptomyces galilaeus and also has potent antineoplastic activity. Aclarubicin: An anthracycline produced by Streptomyces galilaeus. It has potent antineoplastic activity. | aminoglycoside; anthracycline; methyl ester; phenols; polyketide; tetracenequinones; trisaccharide derivative; zwitterion | antimicrobial agent; antineoplastic agent; apoptosis inducer; bacterial metabolite; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor |
| prinomastat | prinomastat : A hydroxamic acid that is (3S)-N-hydroxy-2,2-dimethylthiomorpholine-3-carboxamide in which the hydrogen attached to the thiomorpholine nitrogen has been replaced by a [4-(pyridin-4-yloxy)phenyl]sulfonyl group. It is a selective inhibitor with of matrix metalloproteinases (MMPs) 2, 3, 9, 13, and 14. prinomastat: a diazepine-based hydroxamic acid inhibitor; matrix metalloproteinase (MMP) inhibitor; angiogenesis inhibitor; | aromatic ether; hydroxamic acid; pyridines; sulfonamide; thiomorpholines | antineoplastic agent; EC 3.4.24.35 (gelatinase B) inhibitor; matrix metalloproteinase inhibitor |
| isoliquiritigenin | chalcones | antineoplastic agent; biological pigment; EC 1.14.18.1 (tyrosinase) inhibitor; GABA modulator; geroprotector; metabolite; NMDA receptor antagonist | |
| caffeic acid | trans-caffeic acid : The trans-isomer of caffeic acid. | caffeic acid | geroprotector; mouse metabolite |
| 4-thiouracil | |||
| rs-130830 | RS-130830: orally-active broad-spectrum matrix metalloproteinase inhibitor | ||
| pnu 142372 | |||
| pnu 107859 | |||
| quercetin | 7-hydroxyflavonol; pentahydroxyflavone | antibacterial agent; antineoplastic agent; antioxidant; Aurora kinase inhibitor; chelator; EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor; geroprotector; phytoestrogen; plant metabolite; protein kinase inhibitor; radical scavenger | |
| luteolin | 3'-hydroxyflavonoid; tetrahydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antineoplastic agent; apoptosis inducer; c-Jun N-terminal kinase inhibitor; EC 2.3.1.85 (fatty acid synthase) inhibitor; immunomodulator; nephroprotective agent; plant metabolite; radical scavenger; vascular endothelial growth factor receptor antagonist | |
| amentoflavone | biflavonoid; hydroxyflavone; ring assembly | angiogenesis inhibitor; antiviral agent; cathepsin B inhibitor; P450 inhibitor; plant metabolite | |
| robustaflavone | robustaflavone : A biflavonoid that is obtained by oxidative coupling of two molecules of apigenin resulting in a bond between positions C-3 of the hydroxyphenyl ring and C-6 of the chromene ring. Isolated from Thuja orientalis and Rhus succedanea it exhibits antioxidant, cytotoxic and anti-hepatitis B activity. robustaflavone: bis-apigenin coupled at 6 and 3' positions; a potential non-nucleoside anti-hepatitis B agent; | biflavonoid; hydroxyflavone; ring assembly | anti-HBV agent; antineoplastic agent; antioxidant; metabolite |
| trans-2,3',4,5'-tetrahydroxystilbene | trans-2,3',4,5'-tetrahydroxystilbene: hydroxystilbene oxyresveratrol | stilbenoid | |
| ginkgolic acid | hydroxybenzoic acid | ||
| tmi-1 | |||
| bilobetin | bilobetin: a phospholipase A2 antagonist | flavonoid oligomer | |
| batimastat | batimastat : A secondary carboxamide resulting from the formal condensation of the carboxy group of (2S,3R)-5-methyl-3-{[(2S)-1-(methylamino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-2-[(thiophen-2-ylsulfanyl)methyl]hexanoic acid with the amino group of hydroxylamine. It a broad-spectrum matrix metalloprotease inhibitor. batimastat: structure given in first source; a synthetic matrix metalloproteinase inhibitor | hydroxamic acid; L-phenylalanine derivative; organic sulfide; secondary carboxamide; thiophenes; triamide | angiogenesis inhibitor; antineoplastic agent; matrix metalloproteinase inhibitor |
| isoacteoside | isoacteoside: a phenylethanoid glycoside isolated from Indian paintbrush (Verbenaceae) Castilleja linariaefolia; also in other plants; structure given in first source | hydroxycinnamic acid | |
| Methyl rosmarinate | hydroxycinnamic acid | ||
| ik 682 | IK 682: inhibits TNF-alpha converting enzyme; structure in first source | hydroxamic acid; pyrrolidin-2-ones; quinolines | |
| bay 12-9566 | Bay 12-9566: an angiogenesis inhibitor with matrix metalloproteinase inhibitory activity | biphenyls; organochlorine compound | |
| chlorhexidine | chlorhexidine : A bisbiguanide compound with a structure consisting of two (p-chlorophenyl)guanide units linked by a hexamethylene bridge. Chlorhexidine: A disinfectant and topical anti-infective agent used also as mouthwash to prevent oral plaque. | biguanides; monochlorobenzenes | antibacterial agent; antiinfective agent |
| epigallocatechin-3-o-(3''-o-methyl)-gallate | catechin | ||
| (11c)cgs 25966 | |||
| bb-78485 | BB-78485: structure in first source | ||
| ro 32-3555 | Ro 32-3555: structure given in first source | ||
| ro 28-2653 | Ro 28-2653: a synthetic matrix metalloproteinase inhibitor reduces tumor growth and prolongs survival in a prostate cancer standard rat model | ||
| abt-770 | ABT-770: structure in first source | ||
| proanthocyanidin a1 | procyanidin A1: from aqueous extract of peanut skin; structure in first source | flavonoid oligomer | |
| sb 3ct compound | SB 3CT compound: a matrix metalloproteinase-2 inhibitor; structure in first source | aromatic ether | |
| pd 166793 | |||
| sc 78080 | |||
| ro 31-9790 | Ro 31-9790: hydroxamic acid derivative | ||
| n-((2s)-2-mercapto-1-oxo-4-(3,4,4- trimethyl-2,5-dioxo-1-imidazolidinyl)butyl)-l-leucyl-n,3- dimethyl-l-valinamide | N-((2S)-2-mercapto-1-oxo-4-(3,4,4- trimethyl-2,5-dioxo-1-imidazolidinyl)butyl)-L-leucyl-N,3- dimethyl-L-Valinamide: matrix metalloproteinase inhibitor | ||
| 2-[[4-(4-bromophenyl)phenyl]sulfonylamino]-3-methylbutanoic acid | biphenyls; organobromine compound | ||
| arp-100 | |||
| kb r8301 | |||
| ageladine a | ageladine A : An imidazopyridine that is 1H-imidazo[4,5-c]pyridin-2-amine substituted by a 4,5-dibromo-1H-pyrrol-2-yl group at position 4. It is an alkaloid isolated from a marine sponge Agelas nakamurai and acts as an inhibitor of the matrix metalloproteinases, the key enzymes involved in tumour growth, migration, angiogenesis, invasion and metastasis. Ageladine A: an antiangiogenic matrixmetalloproteinase inhibitor from the marine sponge Agelas nakamurai; structure in first source | alkaloid; aromatic amine; imidazopyridine; organobromine compound; pyrroles | angiogenesis inhibitor; antineoplastic agent; matrix metalloproteinase inhibitor; metabolite |
| s 3304 | S 3304: structure in first source | ||
| N(2)-([biphenyl]-4-ylsulfonyl)-N-hydroxy-N(2)-isopropoxy-D-valinamide | N(2)-([biphenyl]-4-ylsulfonyl)-N-hydroxy-N(2)-isopropoxy-D-valinamide : A hydroxamic acid that is N-hydroxy-D-valinamide in which the alpha-amino group has been substituted by isopropoxy and [biphenyl]-4-ylsulfonyl groups. A selective matrix metalloproteinase-2 (MMP-2) inhibitor, it is one of the most potent inducers of autophagy. Its physiological roles include angiogenesis, cancer metastasis, embryogenesis, tissue remodeling in development, and wound healing. | D-valine derivative; hydroxamic acid | antineoplastic agent; autophagy inducer; EC 3.4.24.24 (gelatinase A) inhibitor; melanin synthesis inhibitor |
| bms-566394 | BMS-566394: structure in first source | ||
| ks370g | KS370G: antihyperglycemic; structure in first source | ||
| incb3619 | INCB3619: ADAM inhibitor; structure in first source | ||
| tosedostat | carboxylic ester; hydroxamic acid; secondary carboxamide | ||
| WAY-316606 | WAY-316606 : A sulfonamide resulting from the formal condensation of the sulfonic acid group of 5-(phenylsulfonyl)-2-(trifluoromethyl)benzenesulfonic acid with the primary amino group of piperidin-4-amine. An inhibitor of secreted Frizzled-Related Protein-1 (sFRP-1). | (trifluoromethyl)benzenes; piperidines; secondary amino compound; sulfonamide; sulfone | secreted frizzled-related protein 1 inhibitor |
| alendronate sodium | |||
| grassystatin a | grassystatin A: isolated from a cyanobacterium, identified as Lyngbya cf.; structure in first source | ||
| (4-(n-hydroxyamino)-2r-isobutyl-3s-methylsuccinyl)-l-phenylglycine-n-methylamide | KB R7785: structure in first source | ||
| phosphomannopentaose sulfate | phosphomannopentaose sulfate: structure in first source | ||
| tetracycline | tetracycline : A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. Tetracycline: A naphthacene antibiotic that inhibits AMINO ACYL TRNA binding during protein synthesis. | ||
| guanosine diphosphate | Guanosine Diphosphate: A guanine nucleotide containing two phosphate groups esterified to the sugar moiety. | guanosine 5'-phosphate; purine ribonucleoside 5'-diphosphate | Escherichia coli metabolite; mouse metabolite; uncoupling protein inhibitor |