Cube-Rhombellane Related Structures: A Drug Perspective

Abstract

Rhombellanes represent a new class of structures, of which homeomorphs may be synthesized as real molecules. Cube-rhombellane is a double-shell structure, with vertices of degree 3 and 6, respectively. Several hypothetical structures/molecules were proposed and computed using molecular graph theory and coordination chemistry principles. Some geometries were optimized at the B3LYP/6-31G (d, p) level of theory, followed by harmonic vibrational frequency analysis at the same level of theory, single point data were collected in view of molecular stability evaluation. Some of the bioactive functionalized structures were also proposed and explored by molecular mechanics (MM)-based conformational analysis, to check their internal mobility. Drug-like properties of the proposed molecular structures were compared with some existing nano-molecules (fullerenes, nanotubes). ADME and other physico-chemical characteristics were computed using commercial software. Substructures of the proposed molecules, useful in a future synthesis, were provided by retro combinatorial synthesis (RECAP). Computational results obtained are promising regarding ADME properties, drug-likeness and nano-properties.

The Immobilization of ChEMBL474807 Molecules Using Different Classes of Nanostructures

“…The ligand molecule, namely ChEMBL474807 (1-(4-amino-1,2,5-oxadiazol-3-yl)-5-(piperidin-1ylmethyl)-N -(pyridin-4-ylmethylene)-1H-1,2,3-triazole-4-carbohydrazide), was obtained from CHEMBL Database [34]. Rhombellane homeomorphs, were obtained from Topo Cluj Group [33], the C 60 structure was downloaded from Brookhaven Protein Database PDB [35], and C 60 functionalized derivatives were obtained from the PubChem database [36]. The carbon nanotubes described in Table 1 were generated using the VMD package [37], chosen values of "n" and "m" vectors allowed for the creation of different types of nanotubes characterized by similar diameter values.…”

“…The characteristic structure of these nanosystems is created by rolling up graphene sheets, and such large surfaces consisting of aromatic systems could exhibit high affinity toward the considered ligand molecule that exhibiting significant activity in stacking interactions. The last interesting group of nanocarriers are the cube rhombellane (Cube-rbl) homeomorphs, consisting of a molecule core and a second shell created by eight modules connected with the structure by three chemical bonds, e.g., ester or amide [30][31][32][33]. The examples of such structures created by Diudea are presented in Figure 2.…”

Docking of Polyethylenimines Derivatives on Cube Rhombellane Functionalized Homeomorphs

“…PEI despite the fact that are cytotoxic [11], have many applications, first of all, as transfection reagents [12]. Calculations at the B3LYP/6-31G (d, p) level of theory [16][17][18][19] confirmed the hypothesis that rhombellanes are energetically feasible in the hope of a real synthesis [20][21][22][23][24][25][26].…”

Docking of Cisplatin on Fullerene Derivatives and Some Cube Rhombellane Functionalized Homeomorphs

“…The structures of rhombellane homeomorphs were prepared by Topo Cluj Group [8][9][10][11][12][13], while the functionalized C 60 structures were downloaded from the PubChem Database [22]. The docking procedure was realized with the use of non-commercial docking program AutoDock 4.2 [23,24].…”

“…There are many types of these structures, among which only those have been used which have functional groups that allow attachment of CisPt ( Figure 3). ful_308a4 ful_308b4 Rhombellans are new structures defined by Diudea [8][9][10][11][12][13] with rings in the form of rhombs or squares, which could be an alternative to classical carrier nanostructures. This new class of compounds, having drug-like properties, and creating bio-nano devices, can be suitable for medical chemistry.…”