Towards the online computer-aided design of catalytic pockets

• Published in: Nature chemistry 2019-10, Vol.11 (10), p.872-879
• Main Authors: Falivene, Laura, Cao, Zhen, Petta, Andrea, Serra, Luigi, Poater, Albert, Oliva, Romina, Scarano, Vittorio, Cavallo, Luigi
• Format: Article
• Language: English
• Subjects: 639/638; 639/638/309; 639/638/440; 639/638/77; 639/638/911; Analytical Chemistry; Biocatalysis; Biochemistry; CAD; Catalysis; Catalysts; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Computer aided design; Density Functional Theory; Design; Design modifications; Imaging, Three-Dimensional; Inorganic Chemistry; Internet; Metalloproteins - chemistry; Metalloproteins - metabolism; Organic Chemistry; Perspective; Physical Chemistry; Substrates; Topography
• ISSN: 1755-4330; 1755-4349
• DOI: 10.1038/s41557-019-0319-5

The engineering of catalysts with desirable properties can be accelerated by computer-aided design. To achieve this aim, features of molecular catalysts can be condensed into numerical descriptors that can then be used to correlate reactivity and structure. Based on such descriptors, we have introduced topographic steric maps that provide a three-dimensional image of the catalytic pocket—the region of the catalyst where the substrate binds and reacts—enabling it to be visualized and also reshaped by changing various parameters. These topographic steric maps, especially when used in conjunction with density functional theory calculations, enable catalyst structural modifications to be explored quickly, making the online design of new catalysts accessible to the wide chemical community. In this Perspective, we discuss the application of topographic steric maps either to rationalize the behaviour of known catalysts—from synthetic molecular species to metalloenzymes—or to design improved catalysts. The shape complementarity between the active site of a catalyst and a substrate influences how effectively a reaction can be catalysed. Computational tools can be used to visualize the shape around the active centre of a range of catalysts and the application of such approaches to rationalize the behaviour of known catalysts — and to design new ones — is discussed.