ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:672-683 (registration)

  Tool registration in the ListToolsRequestSchema response, including name, description, and input schema definition.

  {
    name: 'assess_drug_likeness',
    description: 'Assess drug-likeness using Lipinski Rule of Five and other metrics',
    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:793-794 (registration)

  Tool handler dispatch in the CallToolRequestSchema switch statement.

  case 'assess_drug_likeness':
    return await this.handleAssessDrugLikeness(args);

• src/index.ts:1688-1775 (handler)

  The primary handler function that implements the assess_drug_likeness tool logic: fetches ChEMBL compound data, computes Lipinski Rule of Five violations, Veber rules compliance, and generates comprehensive drug-likeness assessment.

  private async handleAssessDrugLikeness(args: any) {
    if (!args || (!args.chembl_id && !args.smiles)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid drug-likeness assessment 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 drug-likeness assessment requires ChEMBL ID',
                smiles: args.smiles,
              }, null, 2),
            },
          ],
        };
      }
  
      const props = molecule.molecule_properties || {};
  
      // Lipinski Rule of Five
      const mw = props.full_mwt || props.molecular_weight || 0;
      const logp = props.alogp || 0;
      const hbd = props.hbd || 0;
      const hba = props.hba || 0;
  
      const lipinskiViolations = [
        mw > 500 ? 'Molecular weight > 500 Da' : null,
        logp > 5 ? 'LogP > 5' : null,
        hbd > 5 ? 'H-bond donors > 5' : null,
        hba > 10 ? 'H-bond acceptors > 10' : null,
      ].filter(v => v !== null);
  
      // Veber rules
      const rtb = props.rtb || 0;
      const psa = props.psa || 0;
      const veberPass = rtb <= 10 && psa <= 140;
  
      // Overall assessment
      const drugLikenessAssessment = {
        chembl_id: molecule.molecule_chembl_id,
        lipinski_rule_of_five: {
          violations: lipinskiViolations.length,
          details: lipinskiViolations.length > 0 ? lipinskiViolations : ['All criteria met'],
          pass: lipinskiViolations.length === 0,
          criteria: {
            molecular_weight: { value: mw, limit: 500, pass: mw <= 500 },
            logp: { value: logp, limit: 5, pass: logp <= 5 },
            hbd: { value: hbd, limit: 5, pass: hbd <= 5 },
            hba: { value: hba, limit: 10, pass: hba <= 10 },
          },
        },
        veber_rules: {
          pass: veberPass,
          criteria: {
            rotatable_bonds: { value: rtb, limit: 10, pass: rtb <= 10 },
            psa: { value: psa, limit: 140, pass: psa <= 140 },
          },
        },
        overall_assessment: {
          drug_likeness: lipinskiViolations.length === 0 ? 'Excellent' : lipinskiViolations.length === 1 ? 'Good' : 'Poor',
          oral_bioavailability: veberPass && lipinskiViolations.length <= 1 ? 'Likely' : 'Uncertain',
          recommendation: this.getDrugLikenessRecommendation(lipinskiViolations.length, veberPass),
        },
        molecular_properties: props,
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(drugLikenessAssessment, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to assess drug-likeness: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:1777-1786 (helper)

  Supporting helper function called by the handler to provide textual recommendation based on the number of Lipinski violations and Veber rule compliance.

  private getDrugLikenessRecommendation(violations: number, veberPass: boolean): string {
    if (violations === 0 && veberPass) {
      return 'Excellent drug-like properties - suitable for oral administration';
    } else if (violations <= 1 && veberPass) {
      return 'Good drug-like properties - likely suitable for development';
    } else if (violations <= 2) {
      return 'Moderate drug-like properties - may require optimization';
    }
    return 'Poor drug-like properties - significant optimization needed';
  }