PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity
June 2015
Families in Gene Neighborhoods
June 2015
Ryanodine Receptor
April 2015
CCR5 and HIV Infection
January 2015
Drug Targets: Bile Acids in Motion
September 2014
Drug Targets: S1R's Ligands and Partners
September 2014
P2Y Receptors and Blood Clotting
September 2014
Bacterial CDI Toxins
June 2014
Glucagon Receptor
April 2014
March 2014
Microbial Pathogenesis: Targeting Drug Resistance in Mycobacterium tuberculosis
February 2014
Design and Discovery: Virtual Drug Screening
January 2014
Cancer Networks: IFI16-mediated p53 Activation
November 2013
G Proteins and Cancer
November 2013
Drug Discovery: Antidepressant Potential of 6-NQ SERT Inhibitors
October 2013
Drug Discovery: Finding Druggable Targets
October 2013
Drug Discovery: Identifying Dynamic Networks by CONTACT
October 2013
Drug Discovery: Modeling NET Interactions
October 2013
Membrane Proteome: GPCR Substrate Recognition and Functional Selectivity
August 2013
Infectious Diseases: Determining the Essential Structome
May 2013
NDM-1 and Antibiotics
May 2013
Microbial Pathogenesis: Computational Epitope Prediction
January 2013
Microbial Pathogenesis: Influenza Inhibitor Screen
January 2013
Microbial Pathogenesis: Measles Virus Attachment
January 2013
Cytochrome Oxidase
November 2012
Membrane Proteome: The ABCs of Transport
November 2012
Bacterial Phosphotransferase System
October 2012
Regulatory insights
September 2012
Solute Channels
September 2012
Pocket changes
July 2012
Receptor bias
July 2012
Anthrax Stealth Siderophores
June 2012
G Protein-Coupled Receptors
May 2012
Substrate specificity sleuths
April 2012
Reading out regioselectivity
December 2011
Superbugs and Antibiotic Resistance
December 2011
Terminal activation
December 2011
A change to resistance
November 2011
Docking and rolling
October 2011
Breaking down the defenses
September 2011
A2A Adenosine Receptor
May 2011
Cell wall recycler
May 2011
Subtly different
March 2011
January 2011
Subtle shifts
January 2011
ABA receptor diversity
November 2010
COX inhibition: Naproxen by proxy
November 2010
Zinc Transporter ZntB
July 2010
Peptidoglycan binding: Calcium-free killing
June 2010
Treating sleeping sickness
May 2010
Bacterial spore kinase
April 2010
Antibiotics and Ribosome Function
March 2010
Safer Alzheimer's drugs?
March 2010
Anthrax evasion tactics
September 2009
GPCR subunits: Separate but not equal
September 2009
Antibiotic target
August 2009
Salicylic Acid Binding Protein 2
August 2009
July 2009
Tackling influenza
June 2009
Bacterial Leucine Transporter, LeuT
May 2009
Anthrax stealth molecule
March 2009
Drug targets to aim for
February 2009
High-energy storage system
February 2009
Transporter mechanism in sight
February 2009
Scavenger Decapping Enzyme DcpS
November 2008
Blocking AmtB
September 2008

Research Themes Drug discovery

Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity

SBKB [doi:10.1038/sbkb.2015.17]
Featured Article - June 2015
Short description: Reconstructed ancient ancestors of Src and Abl shed light on Gleevec's specificity.

Structures of Gleevec bound to Src (PDB 2OIQ), the ancestral kinase ANC-AS (PDB 4CSV), and Abl (PDB 1OPJ) show how only the P-loop in Abl can lock down the drug. Figure from ref. 1 , reprinted with permission from AAAS.

Kinases have a strongly conserved catalytic domain structure, yet the cancer drug Gleevec shows high selectivity towards Abl kinase, with 103-lower affinity for closely related kinases such as Src. It has been proposed that Gleevec binding induces a global conformational change that differs between Abl and Src, but both modeling- and domain-swapping experiments have failed to identify the basis of specificity.

As protein function reflects not only its sequence and structure but also its energy landscape, Kern and colleagues decided to take an orthogonal approach. Reasoning that both Abl and Src kinases share a common ancestor, they postulated that not just specific residues, but also the surrounding amino acids would be important in sculpting the distinct energy landscapes of the kinases during evolution. They therefore used a Bayesian phylogenetic approach to design four potential ancestral proteins of Abl and Src. These proteins were constructed and shown to have intermediate Gleevec-binding affinities. Overall, the kinetic scheme of the ancestral proteins is the same as that of modern kinases, but the conformational steps (i.e. kinetic parameters) are altered in concert with the affinity changes. This reflects a progressive shift in conformational equilibrium between two bound states; differences in this dynamic process of the kinase/drug complex, but not binding/dissociation rates, are primarily responsible for selectivity.

Structural analysis of the last common ancestor, ANC-AS, helped identify globally distributed amino acid changes responsible for selectivity. In particular, modifying 15 amino acids in the N-terminal domain of ANC-AS (to generate ANC-AS(+15)) increased the Gleevec affinity to equal that of Abl; those amino acid residues underlie most of the change in the equilibrium towards Abl's inhibitor-bound, induced-fit state. Mapping those 15 amino acid changes onto the crystal structure of ANC-AS emphasizes why the basis of selectivity had been so difficult to determine: many of the 15 residues are removed from the binding pocket and form a hydrogen bond network in ANC-AS that cannot occur in ANC-AS(+15) or Abl. The authors speculated that in the absence of this network, the conserved P-loop has mobility and can close over the drug, whereas with the network, the P-loop is stabilized in a different conformation. The concept that the P-loop may be involved in discrimination was previously tested in domain-swapping experiments, but those experiments did not include these 15 residues that were identified from the ancestral reconstruction.

In conclusion, this study illustrates not only the important role that evolutionary reconstruction can offer in identifying key elements that allow for atomistic discrimination of ligands, but also indicates that energy landscapes are a driving force in evolution.

Angela K. Eggleston


  1. C. Wilson et al. Using ancient protein kinases to unravel a modern cancer drug's mechanism.
    Science. 347, 882-6 (2015). doi:10.1126/science.aaa1823

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health