predict_solubility

Predict aqueous solubility and permeability properties for chemical compounds using ChEMBL IDs or SMILES strings to assess bioavailability and drug-likeness.

Instructions

Predict aqueous solubility and permeability properties

Input Schema

TableJSON Schema

Name	Required	Description	Default
`chembl_id`	No	ChEMBL compound ID
`smiles`	No	SMILES string (alternative to ChEMBL ID)

Implementation Reference

src/index.ts:1584-1674 (handler)

The handler function for the 'predict_solubility' tool. Fetches molecule data from ChEMBL API using chembl_id, extracts properties like alogp, psa, etc., applies simple rules to predict solubility class and permeability, and returns formatted JSON response.

private async handlePredictSolubility(args: any) {
  if (!args || (!args.chembl_id && !args.smiles)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid solubility prediction arguments');
  }

  try {
    let molecule;
    if (args.chembl_id) {
      const response = await this.apiClient.get(`/molecule/${args.chembl_id}.json`);
      molecule = response.data;
    } else {
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({
              message: 'SMILES-based solubility prediction requires ChEMBL ID',
              smiles: args.smiles,
            }, null, 2),
          },
        ],
      };
    }

    const props = molecule.molecule_properties || {};

    // Predict solubility based on molecular properties
    const logp = props.alogp || 0;
    const psa = props.psa || 0;
    const mw = props.full_mwt || props.molecular_weight || 0;
    const hbd = props.hbd || 0;
    const hba = props.hba || 0;

    // Simple solubility prediction model
    let solubilityClass = 'Moderate';
    let permeability = 'Moderate';

    if (logp < 0 && psa > 100) {
      solubilityClass = 'High';
      permeability = 'Low';
    } else if (logp > 5 || psa < 40) {
      solubilityClass = 'Low';
      permeability = 'High';
    } else if (logp > 3 && psa < 70) {
      solubilityClass = 'Low-Moderate';
      permeability = 'High';
    } else if (logp < 2 && psa > 80) {
      solubilityClass = 'Moderate-High';
      permeability = 'Low-Moderate';
    }

    const solubilityPrediction = {
      chembl_id: molecule.molecule_chembl_id,
      aqueous_solubility: {
        predicted_class: solubilityClass,
        logp: logp,
        psa: psa,
        factors: {
          lipophilicity: logp > 3 ? 'High (reduces solubility)' : 'Moderate',
          polar_surface_area: psa > 100 ? 'High (increases solubility)' : 'Moderate',
          hydrogen_bonding: `${hbd} donors, ${hba} acceptors`,
        },
      },
      permeability: {
        predicted_class: permeability,
        assessment: this.assessPermeability(props),
      },
      molecular_properties: {
        molecular_weight: mw,
        alogp: logp,
        psa: psa,
        hbd: hbd,
        hba: hba,
      },
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(solubilityPrediction, null, 2),
        },
      ],
    };
  } catch (error) {
    throw new McpError(
      ErrorCode.InternalError,
      `Failed to predict solubility: ${error instanceof Error ? error.message : 'Unknown error'}`
    );
  }
}

src/index.ts:661-670 (schema)

Input schema definition for the predict_solubility tool, allowing optional chembl_id or smiles.

name: 'predict_solubility',
description: 'Predict aqueous solubility and permeability properties',
inputSchema: {
  type: 'object',
  properties: {
    chembl_id: { type: 'string', description: 'ChEMBL compound ID' },
    smiles: { type: 'string', description: 'SMILES string (alternative to ChEMBL ID)' },
  },
  required: [],
},

src/index.ts:792-792 (registration)
Registration of the predict_solubility handler in the CallToolRequestSchema switch statement.
```
return await this.handlePredictSolubility(args);
```

src/index.ts:1676-1686 (helper)

Helper function used by the handler to assess membrane permeability based on PSA and logP.

private assessPermeability(props: any): string {
  const psa = props.psa || 0;
  const logp = props.alogp || 0;

  if (psa < 90 && logp > 0 && logp < 5) {
    return 'Good membrane permeability predicted';
  } else if (psa > 140 || logp < -1) {
    return 'Poor membrane permeability predicted';
  }
  return 'Moderate membrane permeability predicted';
}

ChEMBL MCP Server