A foundational theoreticalAl12E12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications

Abstract

This combined Al₁₂E₁₂ (E = N, P) surface adsorption and docking study describes the new possibility of prospective potential probing(photophysical/optical) and therapy(medicinal/biochemical) with these adsorbent conjugates. DFT investigations were undertaken herein to help generate geometrical models and better understand the possible favorable adsorption energetics. We attempt to explain their adsorption behaviors and docking involving SARS–CoV–2 viruses (PDB)to assess their possible pharmaceutical potential against the pandemic virus (COVID–19). The adsorption behavior of 8–hydroxy–2–methylquinoline (MQ) and its halogenated derivatives, 5,7–diiodo–8–hydroxy–2–methylquinoline (MQI), 5,7–dichloro–8–hydroxy–2–methylquinoline (MQCl), and 5,7–dibromo–8–hydroxy–2–methylquinoline (MQBr), with aluminum–nitrogen (AlN), and aluminum–phosphorous (AlP) fullerene–like nanocages is reported. A decrease in the hardness of the nanoclusters when adsorbed with drug molecules resulted in an incrementally improved chemical softness (see e.g., Hard–Soft Acid Base theory) indicating that reactivity of the drug molecule in the resulting complex increases upon cluster chemical adsorption. The energy gap is found to be maximized for AlN–MQ and minimized for AlP–MQI; the reduced density gradient (RDG) iso–surfaces and AIM studies also corroborated this. Therefore, these two were found, respectively, to be the least and most electrically conductive of the species under study. We selected a simple medicinal building block (chelator)in addition to selecting the cluster based on previous literature reports. Important parameters such as gap energies and global indices were determined. We assessed NLO properties. The SARS–CoV–2 virus PDB docking data for 6VW1, 6VYO, 6WKQ, 7AD1, 7AOL, 7B3C, were enlisted as ligand targets for studies of docking (PatchDock Server) using the requisite PDB geometries (For the structure of 6VW1, kindly see reference, 2020 For the structure of 6VW1, kindly see reference, Shang, J. , Ye, G. , Shi, K. , Wan, Y. , Luo, C. , Aihara, H. , Geng, Q. , Auerbach, A. , & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature 22, 221–224. https://doi.org/10.1038/s41586-020-2179-y [Google Scholar] ; For the structure of 6VYO kindly see reference, 2020 For the structure of 6VYO kindly see reference, Chang, C. , Michalska, K. , Jedrzejczak, R. , Maltseva, N. , Endres, M. , Godzik, A. , Kim, Y. , & Joachimiak, A. (2020). Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2, RCSB PDB. https://doi.org/10.2210/pdb6VYO/pdb. [Google Scholar] ; For the structure of 6WKQ kindly see reference, 2020 For the structure of 6WKQ kindly see reference, Rosas-lemus, M. , Minasov, G. , Shuvalova, L. , Inniss, N. L. , Kiryukhina, O. , Brunzelle, J. , & Satchell, K. J. F. (2020). High resolution structures of the SARS-CoV-2 2’-O-methyltransferase reveal strategies for structure based inhibitor design. Science Signaling, 13(651), eabe1202. https://doi.org/10.1126/scisignal.abe1202. [Web of Science ®] , [Google Scholar] ; For the structure of 7AD1 kindly see reference, 2021 For the structure of 7AD1 kindly see reference, Juraszek, J. , Rutten L. , Blokland, S. , Bouchier, P. , Voorzaat, R. , Ritschel, T. , Bakkers, M. J. G. , Renault, L. L. R. , & Langedijk, J. P. M. (2021). Stabilizing the closed SARS-CoV-2 spike trimer. Nature Communications, 12, 244. https://doi.org/10.1038/s41467-020-20321-x. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] ; For the structure of 7AOL kindly see reference, 2021 For the structure of 7AOL kindly see reference, Guenther, S. , Reinke, P. , & Oberthuer, D. (2021). X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 372, 642–646. https://doi.org/10.1126/science.abf7945. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] ; For the structure of 7B3C kindly see reference, 2021 For the structure of 7B3C kindly see reference, Kokic, G. , Hillen, H. S. , Tegunov, D. , Dienemann, C. , Seitz, F. , Schmitzova, J. , Farnung, L. , Siewert, A. , Hobartner, C. , & Cramer, P. (2021). Mechanism of SARS-CoV-2 polymerase stalling by remdesivir, Nature Communications, 12, 279. https://doi.org/10.1093/bib/bbaa378 [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] ). Such findings indicate that the AlN–drug conjugation have inhibitory effect against these selected receptors. Graphical Abstract Communicated by Ramaswamy H. Sarma