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Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

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Abstract

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein–ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein–ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

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Abbreviations

3D:

Three-dimensional

CATH:

Class Architecture Topology Homologous superfamily

H-bonds:

Hydrogen bonds

MMFF94:

Merck Molecular Force Field

PDB:

Protein Data Bank

PRI:

Protein Recognition Index

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Acknowledgements

This research was supported by funding from the Great Lakes Fishery Commission (Project ID: 2015_KUH_54031). We gratefully acknowledge OpenEye Scientific Software (Santa Fe, NM) for providing academic licenses for the use of their QUACPAC (molcharge) and OEChem software. We also thank the following lab graduates for their contributions to this research: Dr. Maria Zavodszky (now at GE Global Research Center), who observed that hydroxyl-rich ligands tended to result in false positives in screening, Dr. Amy Cayemberg McQuade (now at Carroll University) for carrying out the statistical analysis of protein-water-ligand hydrogen-bond bridges, and Dr. Jeffrey VanVoorst (now at Veritas Technologies, LLC) for developing the non-homologous dataset of 136 protein-small molecule complexes analyzed here. We thank Dr. Michael Feig (Michigan State University) for discussions on the biological basis for the prevalence of oxygen versus nitrogen in natural ligands and also appreciate the data he provided on the atomic composition of metabolites in Mycoplasma genitalium.

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Authors and Affiliations

  1. Protein Structural Analysis and Design Lab, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA

    Sebastian Raschka, Alex J. Wolf, Joseph Bemister-Buffington & Leslie A. Kuhn

  2. Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA

    Leslie A. Kuhn

Authors
  1. Sebastian Raschka
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  2. Alex J. Wolf
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  4. Leslie A. Kuhn
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Correspondence to Leslie A. Kuhn.

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Raschka, S., Wolf, A.J., Bemister-Buffington, J. et al. Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes. J Comput Aided Mol Des 32, 511–528 (2018). https://doi.org/10.1007/s10822-018-0105-2

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