Toxicology knowledge graph for structural birth defects.

BACKGROUND: Birth defects are functional and structural abnormalities that impact about 1 in 33 births in the United States. They have been attributed to genetic and other factors such as drugs, cosmetics, food, and environmental pollutants during pregnancy, but for most birth defects there are no known causes. METHODS: To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes. Specifically, we gathered data from drug/birth-defect associations from co-mentions in published abstracts, gene/birth-defect associations from genetic studies, drug- and preclinical-compound-induced gene expression changes in cell lines, known drug targets, genetic burden scores for human genes, and placental crossing scores for small molecules. RESULTS: Using ReproTox-KG and semi-supervised learning (SSL), we scored >30,000 preclinical small molecules for their potential to cross the placenta and induce birth defects, and identified >500 birth-defect/gene/drug cliques that can be used to explain molecular mechanisms for drug-induced birth defects. The ReproTox-KG can be accessed via a web-based user interface available at https://maayanlab.cloud/reprotox-kg . This site enables users to explore the associations between birth defects, approved and preclinical drugs, and all human genes. CONCLUSIONS: ReproTox-KG provides a resource for exploring knowledge about the molecular mechanisms of birth defects with the potential of predicting the likelihood of genes and preclinical small molecules to induce birth defects.

While birth defects are common, for most birth defects there are no known causes. During pregnancy, developing babies are exposed to drugs, cosmetics, food, and environmental pollutants that may cause birth defects. However, exactly how these environmental factors are involved in producing birth defects is difficult to discern. Also, birth defects can be a consequence of the genes inherited from the parents. We combined general data about human genes and drugs with specific data previously implicating genes and drugs in inducing birth defects to create a knowledge graph representation that connects genes, drugs, and birth defects. This knowledge graph can be used to explore new links that may explain why birth defects occur, particularly those that result from a combination of inherited and environmental influences.

Towards rational syntheses of the elusive metallocarbohedrenes: density functional prescriptions for electronic and geometric structures.

The metallocarbohedrenes are binary molecular clusters containing metal atoms linked by acetylenediide C(2) groups. Hundreds of these molecules have been generated, detected and reacted in the gas phase since the prototype, [Ti(8)(C(2))(6)], was reported in 1992, but none has yet been synthesised pure in bulk: the time gap between detection and preparation increasingly exceeds that of the fullerenes. We report here the results of density functional calculations of geometrical and electronic structure of more than 150 postulated metallocarbohedrenes, stabilised by terminal ligation, in order to recognise the more electronically favourable and less reactive targets. At least 38 metallocarbohedrenes have been identified as having a spin singlet ground state, with a relatively large (> 0.5 eV) energy gap between HOMO and LUMO, and an appropriate HOMO energy. In addition, a considerable number of electronically stable metallocarbohedrenes are predicted to have highly paramagnetic ground states, potentially useful in molecular magnetism. The geometrical principles for enclosing but unstrained coordination of metal sites by terminal ligands are outlined. Mechanisms for rational syntheses are considered in the context of reaction type and precursor selection, including issues of oxidation and reduction, and kinetic versus thermodynamic control. This leads to many diverse reactions suggested for the rational syntheses of metallocarbohedrenes. Some preliminary experimental results are presented.

Preparation of benzyne complexes of group 10 metals by intramolecular suzuki coupling of ortho-metalated phenylboronic esters: molecular structure of the first benzyne-palladium(0) complex.

A series of nickel(II) and palladium(II) aryl complexes substituted in the ortho position of the aromatic ring by a (pinacolato)boronic ester group, [MBr[o-C(6)H(4)B(pin)]L(2)] (M = Ni, L(2) = 2PPh(3) (2a), 2PCy(3) (2b), 2PEt(3) (2c), dcpe (2d), dppe (2e), and dppb (2f); M = Pd, L(2) = 2PPh(3) (3a), 2PCy(3) (3b), and dcpe (3d)), has been prepared. Many of these complexes react readily with KO(t)Bu to form the corresponding benzyne complexes [M(eta(2)-C(6)H(4))L(2)] (M = Ni, L(2) = 2PPh(3) (4a), 2PCy(3) (4b), 2PEt(3) (4c), dcpe (4d); M = Pd, L(2) = 2PCy(3) (5b)). This reaction can be regarded as an intramolecular version of a Suzuki cross-coupling reaction, the driving force for which may be the steric interaction between the boronic ester group and the phosphine ligands present in the precursors 2 and 3. Complex 3d also reacts with KO(t)Bu, but in this case disproportionation of the initially formed eta(2)-C(6)H(4) complex (5d) leads to a 1:1 mixture of a novel dinuclear palladium(I) complex, [(dcpe)Pd(mu(2)-C(6)H(4))Pd(dcpe)] (6), and a 2,2'-biphenyldiyl complex, [Pd(2,2'-C(6)H(4)C(6)H(4))(dcpe)] (7d). Complexes 2a, 3b, 3d, 4b, 5b, 6, and 7d have been structurally characterized by X-ray diffraction; complex 5b is the first example of an isolated benzyne-palladium(0) species.

The seven-membered nickelacycle [NiBr=(o-CH=C(CF3)C6H4CH2PPh2-kappa2C,P)(PPh(CH2Ph)2)].

The crystal and molecular structures of the title compound, 3-bromo-3-(dibenzylphenylphosphonio)-2,2-diphenyl-5-trifluoromethyl-1H-benzo[e][1,2]phosphanickelepine, [NiBr(C(22)H(17)F(3)P)(C(20)H(19)P)], which was obtained as the major regioisomer from insertion of HCCCF(3) into the Ni-C bond of the five-membered phosphanickelacycle [NiBr(o-C(6)H(4)CH(2)PPh(2)-kappa2C,P)(PPh(CH(2)Ph)(2))], have been determined. Principal geometric data include the Ni-X bond lengths Ni-Br 2.3343 (4) A, Ni-P 2.1867 (7) and 2.2094 (7) A, and Ni-C 1.882 (3) A, and the two trans angles P-Ni-P 171.55 (3) degrees and Br-Ni-C 176.88 (9) degrees.