Estimation of the size of drug-like chemical space based on GDB-17 data


The goal of this paper is to estimate the number of realistic drug-like molecules which could ever be synthesized. Unlike previous studies based on exhaustive enumeration of molecular graphs or on combinatorial enumeration preselected fragments, we used results of constrained graphs enumeration by Reymond to establish a correlation between the number of generated structures (M) and the number of heavy atoms (N): logM = 0.584 × N × logN + 0.356. The number of atoms limiting drug-like chemical space of molecules which follow Lipinsky’s rules (N = 36) has been obtained from the analysis of the PubChem database. This results in M ≈ 1033 which is in between the numbers estimated by Ertl (1023) and by Bohacek (1060).

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Authors thank Dr. I. Baskin, Prof. I. Antipin and Dr. G. Marcou for valuable comments. PP thanks the French Embassy in Ukraine for the support of his stay at the University of Strasbourg in 2012. TM acknowledges Kazan Federal University for the support of his stay at the University of Strasbourg in 2012.

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Correspondence to A. Varnek.

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Polishchuk, P.G., Madzhidov, T.I. & Varnek, A. Estimation of the size of drug-like chemical space based on GDB-17 data. J Comput Aided Mol Des 27, 675–679 (2013).

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  • Chemical space
  • Drug-like chemical space
  • Graphs enumeration