Nuclear magnetic resonance assembly of chemical entities

A method for obtaining a focused library of candidate binding compounds, wherein the members of the protein family bind a common ligand, comprising the steps of:

• (a) providing a plurality of samples comprising the protein and a first ligand under conditions wherein the first ligand and the protein form a bound complex, wherein the protein is a member of a family of proteins that bind a common ligand;
• (b) assaying a population of candidate second ligands for the ability to transfer magnetization to the first ligand in a sample from the plurality;
• (c) identifying, from the population of candidate second ligands, a second ligand that transfers magnetization to the first ligand, thereby determining that the two ligands are proximal to each other in a ternary bound complex with the protein;
• (d) observing competitive binding between one of the two ligands and the common ligand, thereby determining that the competitive binding ligand binds to the common ligand binding site of the protein;
• and
• (e) obtaining a population of candidate binding compounds comprising the competitive binding ligand, or a fragment thereof, linked to one of a plurality of homologs of the other ligand,
• whereby the population of candidate binding compounds contains binding compounds that bind to members of the protein family.

A method for obtaining a binding compound having specificity for a member of a protein family, wherein the members of the protein family bind a common ligand, comprising the steps of:

• (a) observing competitive binding of the common ligand and a first ligand to a first protein,
• (b) observing competitive binding of the common ligand and a first ligand to a second protein,
• wherein the first and second proteins are members of the protein family, thereby determining that the first ligand binds to the common ligand binding site of the first and second proteins;
• (c) providing a sample comprising the first protein, the first ligand and a second ligand;
• (d) providing a sample comprising the second protein, the first ligand and the second ligand;
• (e) comparing the degree of magnetization transfer between the first ligand and the second ligand for the samples of parts (b) and (c);
• and
• (f) obtaining a binding compound comprising the first ligand, or a fragment thereof, linked to the second ligand, or a fragment thereof,
• whereby the binding compound selectively binds the first protein compared to the second protein.

A method for obtaining a focused library of candidate binding compounds for a protein family, wherein the members of the protein family bind a common ligand, comprising the steps of:

• (a) providing a ligand-probe having an antenna moiety, wherein the ligand-probe binds to the common ligand binding site of a protein, wherein the protein is a member of the protein family;
• (b) providing a sample comprising the protein, the ligand-probe and a second ligand under conditions wherein the ligand-probe, the second ligand and the protein form a bound complex;
• (c) detecting magnetization transfer between the antenna moiety of the ligand-probe and the second ligand in the bound complex, thereby determining that the antenna moiety and second ligand are proximal in the bound complex;
• and
• (d) obtaining a population of candidate binding compounds comprising the ligand-probe, or a fragment thereof, linked to one of a plurality of second ligand homologs,
• whereby the population contains binding compounds that bind to members of the protein family.

A method for obtaining a focused library of candidate binding compounds, wherein the members of the protein family bind a common ligand, comprising the steps of:

• (a) providing a ligand-probe having an antenna moiety, wherein the ligand-probe binds to the common ligand binding site of a protein, wherein the protein is a member of the protein family;
• (b) providing a plurality of samples comprising the protein and the ligand-probe under conditions wherein the ligand-probe and the protein form a bound complex, wherein the protein is a member of a family of proteins that bind a common ligand;
• (c) assaying a population of candidate second ligands for the ability to transfer magnetization to the antenna moiety of the ligand-probe in a sample from the plurality;
• (d) identifying, from the population of candidate second ligands, a second ligand that transfers magnetization to the antenna moiety of the ligand-probe, thereby determining that the two ligands are proximal to each other in a ternary bound complex with the protein;
• and
• (e) obtaining a population of candidate binding compounds comprising the ligand-probe, or a fragment thereof, linked to one of a plurality of homologs of the other ligand,
• whereby the population of candidate binding compounds contains binding compounds that bind to members of the protein family.