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Biophysical limits of protein-ligand binding.

ABSTRACT: In classic work, Kuntz et al. (Proc. Nat. Acad. Sci. USA 1999, 96, 9997-10002) introduced the concept of ligand efficiency. Though that study focused primarily on drug-like molecules, it also showed that metal binding led to the greatest ligand efficiencies. Here, the physical limits of binding are examined across the wide variety of small molecules in the Binding MOAD database. The complexes with the greatest ligand efficiencies share the trait of being small, charged ligands bound in highly charged, well buried binding sites. The limit of ligand efficiency is -1.75 kcal/mol·atom for the protein-ligand complexes within Binding MOAD, and 95% of the set have efficiencies below a "soft limit" of -0.83 kcal/mol·atom. On the basis of buried molecular surface area, the hard limit of ligand efficiency is -117 cal/mol·Å(2), which is in surprising agreement with the limit of macromolecule-protein binding. Close examination of the most efficient systems reveals their incredibly high efficiency is dictated by tight contacts between the charged groups of the ligand and the pocket. In fact, a misfit of 0.24 Å in the average contacts inherently decreases the maximum possible efficiency by at least 0.1 kcal/mol·atom.

SUBMITTER: Smith RD

PROVIDER: S-EPMC3428497 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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Biophysical limits of protein-ligand binding.

Smith Richard D RD Engdahl Alaina L AL Dunbar James B JB Carlson Heather A HA

Journal of chemical information and modeling 20120718 8

In classic work, Kuntz et al. (Proc. Nat. Acad. Sci. USA 1999, 96, 9997-10002) introduced the concept of ligand efficiency. Though that study focused primarily on drug-like molecules, it also showed that metal binding led to the greatest ligand efficiencies. Here, the physical limits of binding are examined across the wide variety of small molecules in the Binding MOAD database. The complexes with the greatest ligand efficiencies share the trait of being small, charged ligands bound in highly ch ...[more]

PMID: 22713103

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Project description:Chemokines are important in macrophage recruitment and the progression of atherosclerosis. The 'M3' chemokine binding protein inactivates key chemokines involved in atherosclerosis (e.g. CCL2, CCL5 and CX3CL1). We aimed to determine the effect of M3 on plaque development and composition. In vitro chemotaxis studies confirmed that M3 protein inhibited the activity of chemokines CCL2, CCL5 and CX3CL1 as primary human monocyte migration as well as CCR2-, CCR5- and CX3CR1-directed migration was attenuated by M3. In vivo, adenoviruses encoding M3 (AdM3) or green fluorescence protein (AdGFP; control) were infused systemically into apolipoprotein (apo)-E-/- mice. Two models of atherosclerosis development were used in which the rate of plaque progression was varied by diet including: (1) a 'rapid promotion' model (6-week high-fat-fed) and (2) a 'slow progression' model (12-week chow-fed). Plasma chemokine activity was suppressed in AdM3-infused mice as indicated by significantly less monocyte migration towards AdM3 mouse plasma ex vivo (29.56%, p = 0.014). In the 'slow progression' model AdM3 mice had reduced lesion area (45.3%, p = 0.035) and increased aortic smooth muscle cell ?-actin expression (60.3%, p = 0.014). The reduction in lesion size could not be explained by changes in circulating inflammatory monocytes as they were higher in the AdM3 group. In the 'rapid promotion' model AdM3 mice had no changes in plaque size but reduced plaque macrophage content (46.8%, p = 0.006) and suppressed lipid deposition in thoracic aortas (66.9%, p<0.05). There was also a reduction in phosphorylated p65, the active subunit of NF-?b, in the aortas of AdM3 mice (37.3%, p<0.0001). M3 inhibited liver CCL2 concentrations in both models with no change in CCL5 or systemic chemokine levels. These findings show M3 causes varying effects on atherosclerosis progression and plaque composition depending on the rate of lesion progression. Overall, our studies support a promising role for chemokine inhibition with M3 for the treatment of atherosclerosis.

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Biophysical limits of protein-ligand binding.

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Biophysical limits of protein-ligand binding.

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