In this work, we developed a computational workflow to mine the Protein Data Bank for isosteric replacements that exist in different binding site environments but have not necessarily been identified and exploited in compound design. Taking phosphate groups as examples, the workflow was used to construct 157 data sets, each composed of a reference protein complexed with AMP, ADP, ATP, or pyrophosphate as well other ligands. Phosphate binding sites appear to have a high hydration content and large size, resulting in U-shaped bioactive conformations recurrently found across unrelated protein families. A total of 16 413 replacements were extracted, filtered for a significant structural overlap on phosphate groups, and sorted according to their SMILES codes, see workflow in Figure 1. In addition to classical isosteres of phosphate, we found unexpected types of replacements that do not conserve charge or polarity, for example phosphate replaced by aliphatic groups, phenyl, or carbamoyl groups. The structural mechanism involved in structural isosteres appears varied: New interactions may be created, water molecules are important, in some case ion plays a role, and of course large and small conformational changes do occur at the binding sites. This study has implications both in the field of medicinal chemistry, i.e. it expands our knowledge of structural isosteres, and in the field of chemoinformatics, since our results have implications with respect to the definitions of chemical similarity.
Structural Isosteres of Phosphate Groups in the Protein Data Bank - ACS DC 2017
1. 1254th American Chemical Society National Meeting08-2017
Structural isosteres of phosphate groups
in the protein data bank
Alexandre Borrel, PhD
Postdoctoral Research Associate,
Department of Chemistry, Bioinformatics Research Center,
North Carolina State University, USA
Division of pharmaceutical chemistry and technology
Faculty of pharmacy
University of Helsinki
@AlBorrel
2. 2254th American Chemical Society National Meeting08-2017
Background: Drug optimization
Hann, M.M. (2011). Medchemcomm 2: 349–355.
Modify a drug to influence
Absorption, Distribution,
Metabolism, Excretion and
Toxicity (ADME-Tox) properties
in preserving an initial
biological activity.Initial hit
Final drug
3. 3254th American Chemical Society National Meeting08-2017
Definitions
(1) Brown, N. (2014). Mol. Inform. 33: 458–462.
Isostere or isosteric replacement (1):
• Preserve biological activity
• Retain the physicochemical or topological properties of the reference compound
Carcinogen Analgesic
Anti-inflammatory
Cheminformatics to propose possible replacement
4. 4254th American Chemical Society National Meeting08-2017
In silico approaches
Propose large databases of bioisosters, ligand based and structure based
sc-PDB-frag (1):
- Structure based
- Interaction fingerprints
KRIPO (2):
- Structure based
- Pharmacophore
fingerprints
SwissBioisostere (3):
- Ligand based
- Molecular pair from
CHEMBL
Hydrophobic
H-bond
(1) Desaphy J, Rognan D (2014) J Chem Inf Model 54:1908–1918. doi: 10.1021/ci500282c
(2) Wood DJ, Vlieg J De, Wagener M, Ritschel T (2012) J Chem Inf Model 52:2031–2043. doi: 10.1021/ci3000776
(3) Wirth M, Zoete V, Michielin O, Sauer WHB (2013). Nucleic Acids Res 41:1137–1143. doi: 10.1093/nar/gks1059
5. 5254th American Chemical Society National Meeting08-2017
Local structural replacements
Chemical groups which occupy the same space
in two homologous superimposed complexes.
Local structural
replacement (LSR)
Superimposed
homologous proteins
6. 6254th American Chemical Society National Meeting08-2017
Study case: phosphate
• Attractive target for therapeutic development (1)
• 30% of the cellular proteins are phosphoproteins,
2,940 of structures available in PDB
• Phosphate group is charged at biological pH, poorly
permeable (2)
Phosphate groups in ATP
(1) Cohen, P. (2000). Trends Biochem. Sci. 25: 596–601.
(2) Smith, F.W., Mudge, S.R., Rae, A.L., and Glassop, D. (2003). Plant Soil 248: 71–83.
7. 7254th American Chemical Society National Meeting08-2017
Computational workflow
Extract from PDB (130,000 structures) complexed
protein which included ligand with a phosphate
group
8. 8254th American Chemical Society National Meeting08-2017
Computational workflow
Filter the PDB
(1,186 structures)
9. 9254th American Chemical Society National Meeting08-2017
Computational workflow
Homologous protein
(Blastp cutoff 10-100)
10,991 structures
16. 16254th American Chemical Society National Meeting08-2017
Isosteres?
Number of atom similar - different
LigandID–PDBIDIC50
Extract affinity information (from congener series)
17. 17254th American Chemical Society National Meeting08-2017
U-shape configuration
U-shape replacements, found in different protein families (binding affinity decreases).
18. 18254th American Chemical Society National Meeting08-2017
Miscellaneous replacements
Hydrophobic and positively charged replacements open perspectives to find not
suspected before.
Hydrophobic replacements
NAD+ truncated (positive)
19. 19254th American Chemical Society National Meeting08-2017
Conclusion
• 15,819 phosphate replacements
• Organization based on target and type of structural replacements
• Mechanisms for phosphate replacements (protein or metal displacement)
• New no suspected replacement (U-shape, hydrophobic, or positively charged)
• Workflow is fully customizable (github)
Zhang, Y.*, Borrel, A.*, Ghemtio, L., Regad, L., Boije af Gennäs, G.,
Camproux, A.-C., et al. (2017). Structural Isosteres of Phosphate Groups in
the Protein Data Bank. J. Chem. Inf. Model. 57: 499–516.
20. 20254th American Chemical Society National Meeting08-2017
Acknowledgments
Authors:
- Yuezhou Zhang
- Leo Ghemtio
- Leslie Regad
- Gustav Boije af Gennäs
- Anne-Claude Camproux
- Jari Yli-Kauhaluoma
- Henri Xhaard*
Fourches’ lab
22. 22254th American Chemical Society National Meeting08-2017
Water molecules versus
RX
• Poorly crystallized
• Present only at very high resolution
(< 1.5 Å)
Datasets from the PDB with 1.5 Å and 3 Å of
resolution
23. 23254th American Chemical Society National Meeting08-2017
Miscellaneous
replacements
Hydrophobic replacements, favour hydrophobic contacts in
binding site.
Positively charged replacement is surprising
considering that the phosphate groups are
negatively charged.
24. 24254th American Chemical Society National Meeting08-2017
Bioisoster replacement
“One of two or more substances related to each other by origin, structure, or
function.” (IUPAC)
Shin, Y., Chen, W., Habel, J., Duckett, D., Ling, Y.Y., Koenig, M., et al. (2009). Bioorganic Med. Chem. Lett. 19: 3344–3347.
A group change and the
affinity (IC50)
25. 25254th American Chemical Society National Meeting08-2017
Hierarchical organization
Dependency of protein target: LSR target based classification
Meanwell, N.A.N.N. a (2011). J. Med. Chem. 54: 2529–2591.
cPLAA2α inhibitor analogs
+ + + - - -
Angiotensin II receptor antagonist analogs
26. 26254th American Chemical Society National Meeting08-2017
Structural replacement
ESP: electrostatic
score potential (1)
= 1: phosphate is
fully covert by the
LSR
LSR superimposition not overlap completely with phosphate groups
27. 27254th American Chemical Society National Meeting08-2017
Replacement
mechanisms
PDB code: 3JZI – 1DV2
28. 28254th American Chemical Society National Meeting08-2017
Replacement
mechanisms
PDB code: 3JZI – 1DV2
29. 29254th American Chemical Society National Meeting08-2017
Replacement mechanisms
PDB code: 3JZI – 1DV2
Protein replaces the phosphate group
30. 30254th American Chemical Society National Meeting08-2017
Chemical replacement
Southall, N.T., and Ajay (2006). J. Med. Chem. 49: 2103–2109
Example of chemical replacements
in kinase patent space from gefitinib
remove
Replaceadd
Editor's Notes
Hello im alexandre Borrel, Im a post doc at north Carolina state university, department of chemisty bioinformatics research center and I will presented you a preject that a do during my thesis at university of helinsik, di…
I will present you a study about the structural isoster of phosphate group in the PDB
Drug optimization
Long process, which consist to modify a drug to transform a hit to a final drug to optimize different properties as potency, safety, metabolomic, specifictu and absoption these modification we need to preserve boological activity
Defintion of isostere, it is a a replacement which replace a group by another one. The affinity is conserved but modification will nfluence the different compound properties
Hovevwe many replacement are possible and different cheminmatics approces were developed to propose some libraity of bioisostere for a chemical group
This different database can be structure or ligand based as for exemple scPDB-frag which study the bindige site and take the replacement that conserve the interaction profile, Kripo also based on fingerprint of interaction and for example Swissbioisostere ligand based based on molecular pairs from chembl
I developed a pproches based on the local structure replace, which non considere a profile of replacement but a structural replacement.
A structural replacement is a group which occupy the same space that the group to replace in 2 homologous superimposed protein.
For exemple you have 2 superimposed protein with 2 ligand and the replacement in green is the group which overlap the phosophate
Considering the hposte, as a interesting target, because 30% are phosphoprotein and there are in the PDB a importeant crystalized phosphate, we develop a complutational workflow to find structural replacement
The workflo is divided in different step. The first consist to extract protein with a phosphate grioup from the PDB
From these protein we applied different filter of resolution and quality
These step define reference protein set
From this protein set we define a set of homologous protein which contains LSR using a blastp.
We superimposed the 2 set and extracted the LSR
From this methods a set of 15 thousand of LSR are extracted and classify to be usefull by the user
The classification is divided in different level, the first one is the ligand containing if for example the LSR include a B ester or another group
The second level is based on the protein where the LSR is find, family name, cluster of identity sequences and reference PDB ID
And for each the databased included ligand, LSR, BS
All of these different strucures are superimpsoed
Elucidate some molecular mechanism
But the question now is to know if these different replacement are isostere. To dicuss about that we propose a matrix for each protein family.
Matrix include different replacement in the protein
For each we have the atom in commun and the different based on MCS analysis and the different LSR in SMILE as well as the affinities where there are available in binding DB
With this database we ppropose in the publicatation different local structural replacement analysis, new perpectivie for the phosphate replacement
Also based on different replacement hydrophobic repacment a well as positively charged replacement