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Showing 121 - 130 of 605359 pathways
SMPDB ID Pathway Name and Description Pathway Class Chemical Compounds Proteins

SMP0000254

Pw000352 View Pathway

Gentamicin Action Pathway

Gentamicin (also known as Garamycin) is an antibiotic that can be used to treat various bacterial infections by inhibiting bacterial protein synthesis. Gentamicin can bind on bacterial 30S ribosomal subunit protein and 16S rRNA irreversibly to inhibit the formation of mRNA. Since the binding site of gentamicin is the region that interacts with wobble base of anticodon of tRNA, hence, binding will cause misreading of mRNA, which lead to incorrect insertion of amino acids to polypeptide so that the polypeptide is non-functional or toxic. This prevents the bacterial protein synthesis which prevent the growth of the bacteria. Gentamicin is a class of aminoglycosides. Aminoglycosides can effectively against aerobic, Gram-negative bacteria, but it is ineffective against anaerobic bacteria, fungi and viruses.
Drug Action

SMP0000259

Pw000357 View Pathway

Streptomycin Action Pathway

Streptomycin (also named Gerox or Agrimycin) is an aminoglycoside antibiotic for the treatment of bacteria infections by inhibiting the synthesis of bacterial proteins. Streptomycin reversibly binds to 16S rRNA and the bacterial 30S ribosomal subunit so that the initiation complex with mRNA couldn't be formed. Binding of streptomycin on 16S rRNA's four nocleotides will lead to misreading of mRNA which result in insertion of incorrect amino acids into polypeptide. Nonfunctional or toxic peptides will lead to nonfunctional monosomes. Aminoglycosides are useful primarily in infections involving aerobic, Gram-negative bacteria, such as Pseudomonas, Acinetobacter, and Enterobacter. In addition, some mycobacteria, including the bacteria that cause tuberculosis, are susceptible to aminoglycosides. Infections caused by Gram-positive bacteria can also be treated with aminoglycosides, but other types of antibiotics are more potent and less damaging to the host. In the past the aminoglycosides have been used in conjunction with penicillin-related antibiotics in streptococcal infections for their synergistic effects, particularly in endocarditis. Aminoglycosides are mostly ineffective against anaerobic bacteria, fungi and viruses.
Drug Action

SMP0000439

Pw000244 View Pathway

Vinorelbine Action Pathway

Vinorelbine (also named Navelbine) is a semisynthetic vinca alkaloid. Vinorelbine are used as chemotherapy medication such as an antimitotic anticancer agent. The mechanism of vinorelbine is the inhibition of microtubule dynamics that would cause mitotic arrest and eventual cell death. As a microtubule destabilizing agent, vinorelbine stimulates mitotic spindle destruction and microtubule depolymerization at high concentrations. At lower clinically relevant concentrations, vinorelbine can block mitotic progression. Unlike the taxanes, which bind poorly to soluble tubulin, vinorelbine can bind both soluble and microtubule-associated tubulin. To be able stabilizing the kinetics of microtule, vinorelbine rapidly and reversibly bind to soluble tubulin which can increase the affinity of tublin by the induction of conformational changes of tubulin. Vinorelbine binds to β-tubulin subunits at the positive end of microtubules at a region called the _Vinca_-binding domain. Binding between vinorelbine and solubale tubulin decreases the rate of microtubule dynamics (lengthening and shortening) and increases the duration of attenuated state of microtubules. Therefore, the proper assembly of the mitotic spindle could be prevented; and the tension at the kinetochores of the chromosomes could be reduced. Subsequently, chromosomes can not progress to the spindle equator at the spindle poles. Progression from metaphase to anaphase is blocked and cells enter a state of mitotic arrest. The cells may then undergo one of several fates. The tetraploid cell may undergo unequal cell division producing aneuploid daughter cells. Alternatively, it may exit the cell cycle without undergoing cell division, a process termed mitotic slippage or adaptation. These cells may continue progressing through the cell cycle as tetraploid cells (Adaptation I), may exit G1 phase and undergo apoptosis or senescence (Adaption II), or may escape to G1 and undergo apoptosis during interphase (Adaptation III). Another possibility is cell death during mitotic arrest. Alternatively, mitotic catastrophe may occur and cause cell death. Vinca alkaloids are also thought to increase apoptosis by increasing concentrations of p53 (cellular tumor antigen p53) and p21 (cyclin-dependent kinase inhibitor 1) and by inhibiting Bcl-2 activity. Increasing concentrations of p53 and p21 lead to changes in protein kinase activity. Phosphorylation of Bcl-2 subsequently inhibits the formation Bcl-2-BAX heterodimers. This results in decreased anti-apoptotic activity. One way in which cells have developed resistance against the vinca alkaloids is by drug efflux. Drug efflux is mediated by a number of multidrug resistant transporters as depicted in this pathway.
Drug Action

SMP0000247

Pw000345 View Pathway

Azithromycin Action Pathway

Azithromycin, trade names include Zithromax and Azithrocin, is a semisynthetic azalide derived from erythromycin. Azalides are part of the macrolide antibiotic class. Azithromycin targets protein synthesis of bacteria by binding to the 50S subunit of the bacterial ribosome to inhibit mRNA translation and prevent bacteria growth. Macrolides are broad spectrum antibiotics. It is prescribed to treat bacterial infections including: sexually transmitted infections like chlamydia, pneumonia, strep throat, ear infections, sinusitis and more.
Drug Action

SMP0111876

Pw112934 View Pathway

Protein Synthesis: Phenylalanine

Protein synthesis is an essential life process that builds the important large amino acid macromolecules that function as enzymes, antibodies, and cellular structural components. Although synthesis begins with the transcription of DNA into RNA, this pathway depicts the reactions that occur during translation. Transcribed messenger RNA (mRNA), which contains the genetic code to direct protein synthesis, is transported out of the nucleus and becomes bound to ribosomes in the cytoplasm or endoplasmic reticulum. The amino acids required to assemble polypeptide chains are delivered to the ribosomes using transfer RNA (tRNA). Each tRNA molecule has both a binding site for a specific amino acid and a three-nucleotide sequence called the anticodon that forms three complementary base pairs with an mRNA codon. Charging or loading the appropriate amino acid onto its tRNA is carried out by an aminoacyl-tRNA synthetase (aaRS or ARS), also called tRNA-ligase. This enzyme catalyzes the esterification of an amino acid to one of all its compatible tRNAs to form an aminoacyl-tRNA. Each of the twenty amino acids has a corresponding aa-tRNA made by a specific aminoacyl-tRNA synthetase. Ribosomes match the anticodons of the charged tRNA molecules with successive codons of the mRNA. After a match is found, the ribosome transfers the amino acid from the matching tRNA onto the growing peptide chain via a reaction termed peptide condensation, and the tRNAs, no longer carrying amino acids, are released.
Protein

SMP0119303

Pw120526 View Pathway

Protein Synthesis: Tryptophan

Protein synthesis is an essential life process that builds the important large amino acid macromolecules that function as enzymes, antibodies, and cellular structural components. Although synthesis begins with the transcription of DNA into RNA, this pathway depicts the reactions that occur during translation. Transcribed messenger RNA (mRNA), which contains the genetic code to direct protein synthesis, is transported out of the nucleus and becomes bound to ribosomes in the cytoplasm or endoplasmic reticulum. The amino acids required to assemble polypeptide chains are delivered to the ribosomes using transfer RNA (tRNA). Each tRNA molecule has both a binding site for a specific amino acid and a three-nucleotide sequence called the anticodon that forms three complementary base pairs with an mRNA codon. Charging or loading the appropriate amino acid onto its tRNA is carried out by an aminoacyl-tRNA synthetase (aaRS or ARS), also called tRNA-ligase. This enzyme catalyzes the esterification of an amino acid to one of all its compatible tRNAs to form an aminoacyl-tRNA. Each of the twenty amino acids has a corresponding aa-tRNA made by a specific aminoacyl-tRNA synthetase. Ribosomes match the anticodons of the charged tRNA molecules with successive codons of the mRNA. After a match is found, the ribosome transfers the amino acid from the matching tRNA onto the growing peptide chain via a reaction termed peptide condensation, and the tRNAs, no longer carrying amino acids, are released.
Protein

SMP0063759

Pw064749 View Pathway

Lysophosphatidic Acid LPA6 Signalling

Lysophosphatidic acid (LPA) is a water-soluble phospholipid derivative and a potent signalling molecule that binds to six known lysophosphatidic acid receptors (LPARs), named LPA1-LPA6. All six receptors belong to the G protein-coupled receptor (GPCR) superfamily which initiates intracellular signalling cascades via four G protein classes differentiated by their α subunit type: Gαs, Gαi/o, Gαq/11, Gα12/13. GPCRs mediate a wide range of biological processes, including cell survival, proliferation, migration, and differentiation, vascular regulation, and cytokine release. Due to LPA's physiological importance, abnormal LPA signalling likely contributes to the pathophysiology of many diseases. LPA biosynthesis proceeds through two major pathways: (1) the conversion of lysophospholipids (e.g. LPC, LPE, LPS) into LPA via autotaxin (ATX/Enpp2) and (2) the conversion of phosphatidic acid (PA) into LPA via phospholipase A1 or A2 (PLA1/PLA2). The binding of LPA to an LPAR allosterically activates the heterotrimeric G protein by exchanging GDP for GTP at the G protein's alpha subunit. This results in the dissociation of a Gα-GTP monomer and a Gβγ dimer from the receptor which allows both complexes to begin signalling cascades via downstream effectors. LPA1 signalling has been implicated in important processes such as cell survival, proliferation, adhesion, migration, immune function, and myelination. This receptor can couple with the G proteins Gαi/o, Gαq/11, and Gα12/13. The Gαi/o subunit inhibits the enzyme adenylyl cyclase (AC) which catalyzes the production of the important secondary messenger 3',5'-cyclic AMP (cAMP) from adenosine triphosphate (ATP). Other downstream effectors of Gαi/o include the MAPK/ERK pathway, the PI3K/Akt pathway, and P13K/Rac signalling. The Gαq/11 subunit activates phospholipase C (PLC) which cleaves the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2) into the secondary messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 diffuses through the cytoplasm to the ER and binds to the inositol 1,4,5-trisphosphate (Ins3P) receptor, releasing calcium from the endoplasmic reticulum into the cytoplasm. Both calcium and DAG activate the kinase activity of protein kinase C beta (PKC). Among many other functions, PKC activates NF-κB. This leads to increased antigen presentation and increased expression of pro-inflammatory cytokines, cell adhesion molecules, and chemotactic factors. The Gα12/13 subunit regulates cell motility and cytoskeletal remodelling by activating the Rho/ROCK and Rho/SRF pathways.
Protein

SMP0069871

Pw070885 View Pathway

BCR Signaling Pathway

The BCR signalling pathway is a pathway that plays a vital role in the development and all other functions of B-cells, which means it is vital for the immune response. The BCR, also known as the B-cell receptor, is usually found on the outer membrane of B-cells. B-cells grab antigens from immune synapses, through a number of processes including cell spreading and receptor transport. After these have been performed, endocytosis and antigen-presentation occur. B-cells manipulate the dynamic of BCR-antigen bonds. They group and spread the antigen, increasing the relation with BCR, which creates sensitivity. The two main functions of the BCR pathway is to signal transduction, and the second is to prepare the antigen for processing by the helper T cells. Any defects in this pathway may lead to the patient being immunodeficient, or having B-cell malignancy.
Protein

SMP0063771

Pw064763 View Pathway

Ahr Signal Transduction Pathway

The aryl hydrocarbon receptor, known as AHR, is a normally cytosolic transcription factor that can bind to foreign compounds such as flavonoids and indoles from foods, as well as synthetic ligands including polychlorobiphenyls (PCBs) and polychlorinated dibenzo-p-dioxins (PCDD). This includes 2,3,7,8-tetrachlorodibenzodioxin (TCDD), which is the ligand shown in this pathway. AHR interacts with heat shock protein 90 (HSP90AA1), which acts as a chaperone for it. After this association, the ligand, in this case TCDD, can form a covalent bond with the complex in the cell's cytoplasm. This binding causes AHR and the rest of the complex to translocate into the nucleus of the cell. Once in the nucleus, the heat shock protein dissociates, leaving binding sites which the AHR nuclear translocator (ARNT) then binds to. Finally, the AHR/ARNT complex can interact, either directly or indirectly, with the DNA, in this case specifically a dioxin response element. With other ligands, the complex will bind to the equivalent DNA that corresponds to the genes that allow metabolism of the ligand.
Protein
  • 2,3,7,8-tetrachlorodibenzo-p-dioxin

SMP0063778

Pw064770 View Pathway

Ion Channels and Their Functional Role in Vascular Endothelium

In endothelial cell, ion channels such as agonist-activated nonselective Ca(2+)-permeable cation channels, cyclic nucleotide-activated nonselective cation channels, and store-operated Ca(2+) channels or capacitative Ca(2+) entry are controlled by intracellular Ca(2+) signals. Some of the channels are expressed by trp gene family. Ca(2+) entry is also controlled by large-conductance Ca(2+)-dependent BK(Ca) channels (slo), inwardly rectifying K(+) channels, Ca(2+)-activated Cl(-) channel and volume-regulated anion channel (VRAC). VRAC channels can also transport organic osmolytes and amino acid.
Protein
Showing 121 - 130 of 65006 pathways