EcoDrug+: an advanced database for drug target conservation analysis and environmental risk assessment

90-Minute Technical Workshop Participant Handout

Case Study: CLOZAPINE

Clozapine is an FDA-approved atypical antipsychotic primarily used for treatment-resistant schizophrenia, where it stands as the most effective medication available. Additionally, it is prescribed to help lower the risk of suicidal behavior in individuals with schizophrenia or schizoaffective disorder. [1]

Module 1

Chemical Selection & Human Target Profiling

Task 1: Chemical Selection & Identification
  • Open the EcoDrug+ platform.
  • Navigate to the Chemical menu or search bar on the landing page.
  • Input the common name or identifier for the compound: Search using Clozapine, CAS RN: 5786-21-0, the ChEMBL ID CHEMBL42 (or use the SMILES string: CN1CCN(C2=Nc3cc(Cl)ccc3Nc3ccccc32)CC1).
  • Note down therapeutic classification of the drug.
Task 2: Human Target Profiling
  • Query Chemical Identifiers Locate Clozapine using standard identifiers (e.g., CAS RN: 5786-21-0 or ChEMBL ID: CHEMBL42) to ensure data accuracy
  • Extract Mechanisms of Action (MoA) Retrieve known primary targets
  • Locate the target HTR2A (5-hydroxytryptamine receptor 2A) and DRD2 (Dopamine receptor D2)

Chemical and primary target information

Chemical information
Search by Name: Clozapine
Search by Identifier:
  • CAS RN: 5786-21-0
  • ChEMBL ID: CHEMBL42

      • Chemical Representation:
      • SMILES: CN1CCN(C2=Nc3cc(Cl)ccc3Nc3ccccc32)CC1
Clozapine Target profile
Primary targets:
Dopamine D2 receptor[2]
  • Gene Symbol: DRD2
  • Gene Name: dopamine receptor D2
  • Chromosomal Location:11q23.2
  • Ensembl Gene : ENSG00000149295
5-HT2A receptor[3]
  • Gene Symbol: HTR2A
  • Gene Name: 5-hydroxytryptamine receptor 2A
  • Chromosomal Location:13q14.2
  • Ensembl Gene : ENSG00000102468
Module 2

Evolutionary Target Conservation & Orthology Mapping

Mapping human drug targets onto 180+ environmental wildlife species using Ensembl-derived phylogenetic comparisons, identifying species vulnerable to unintentional target-mediated toxicity.

Task 1: Executing the Gene Search & Retrieving Orthologs
  • Input Identifiers Enter your selected gene symbol or target
  • Fetch Cross-Species target conservation
  • Analyze the the target conservation (comprising 12–16 distinct taxonomic groups).Shaded or grayed-out icons represent groups where the gene target conservation is entirely absent.
Task 2: Evaluating Conservation Metrics & Sequence Identity
  • Identify the primary targets for the primary targets
  • Select BLAST from selected species from Biochemical menu
  • Set up BLAST parameter
  • Check Sequence Similarity (BLAST Results)
Input data
  • Human target: DRD2 (Dopamine receptor D2) / HTR2A (5-hydroxytryptamine receptor 2A)
  • BLAST sequence : Calculates sequence identity matches to establish read-across the species
      • Examples:
      Dopamine receptor D2
      >sp|P14416|DRD2_HUMAN D(2) dopamine receptor OS=Homo sapiens OX=9606 GN=DRD2 PE=1 SV=2
      MDPLNLSWYDDDLERQNWSRPFNGSDGKADRPHYNYYATLLTLLIAVIVFGNVLVCMAVS REKALQTTTNYLIVSLAVADLLVATLVMPWVVYLEVVGEWKFSRIHCDIFVTLDVMMCTA SILNLCAISIDRYTAVAMPMLYNTRYSSKRRVTVMISIVWVLSFTISCPLLFGLNNADQN ECIIANPAFVVYSSIVSFYVPFIVTLLVYIKIYIVLRRRRKRVNTKRSSRAFRAHLRAPL KGNCTHPEDMKLCTVIMKSNGSFPVNRRRVEAARRAQELEMEMLSSTSPPERTRYSPIPP SHHQLTLPDPSHHGLHSTPDSPAKPEKNGHAKDHPKIAKIFEIQTMPNGKTRTSLKTMSR RKLSQQKEKKATQMLAIVLGVFIICWLPFFITHILNIHCDCNIPPVLYSAFTWLGYVNSA VNPIIYTTFNIEFRKAFLKILHC
      5-hydroxytryptamine receptor 2A
      >sp|P28223|5HT2A_HUMAN 5-hydroxytryptamine receptor 2A OS=Homo sapiens OX=9606 GN=HTR2A PE=1 SV=2 MDILCEENTSLSSTTNSLMQLNDDTRLYSNDFNSGEANTSDAFNWTVDSENRTNLSCEGC LSPSCLSLLHLQEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIAD MLLGFLVMPVSMLTILYGYRWPLPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNP IHHSRFNSRTKAFLKIIAVWTISVGISMPIPVFGLQDDSKVFKEGSCLLADDNFVLIGSF VSFFIPLTIMVITYFLTIKSLQKEATLCVSDLGTRAKLASFSFLPQSSLSSEKLFQRSIH REPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNEDVIGA LLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENKKPLQLILVNTIPALAYK SSQLQMGQKKNSKQDAKTTDNDCSMVALGKQHSEEASKDNSDGVNEKVSCV
BLAST parameter:
  • Scoring matrix: Default BLOSUM62
  • Sequence Identity (%)
  • e-value
  • Query Coverage
Target conservation across-Species
High conservation in fish (e.g., Danio rerio matching >50% identity for neuroreceptors); low or absent matching in invertebrates.
Module 3

Chemical Similarity

Groups structurally related substances (~7.2k pharmaceuticals, 34k agrochemicals, 61k metabolites) into interactive knowldege graphs.

Task 1: Setting Parameters and Running the Query
  • Retrieve Clozapine structural data Obtain the exact structural format required by EcoDrug+. While you can search by text name or identifier (CAS RN: 5786-21-0; ChEMBL ID: CHEMBL42), using the exact SMILES string
  • Open EcoDrug+ and go to the Chemical navigation tab, selecting Chemical Similarity or using the embedded structural drawing panel.
  • Define Search Type & Tanimoto Threshold Choose Similarity Search rather than an Exact or Substructure search. Set your Tanimoto coefficient cutoff (e.g., Threshold >50%) depending on how broadly you want to capture structural analogues
Task 2: Analyzing Clustered Analogues and Generating Knowledge Graphs
  • Extract Clustered Compounds
  • Perform Maximum Common Substructure (MCS) Mapping
  • Generate the Interactive Knowledge Graph
Input data
Search by Name: Clozapine
Search by Identifier:
  • CAS RN: 5786-21-0
  • ChEMBL ID: CHEMBL42

Chemical Representation:

  • SMILES: CN1CCN(C2=Nc3cc(Cl)ccc3Nc3ccccc32)CC1
Parameter
  • Exact
  • Similarity (Tanimoto threshold >= cut off)
  • Substructure
Clozapine similar
Maps closely linked Diazepines, oxazepines, thiazepines and oxepines derivatives (e.g., Olanzapine, Clothiapine, Quetiapine)
Module 4

REST API Endpoints

Fetches compound information, mechanism of action and target conservation across species using the EcoDrug+ preferred name

Task 1: Fetch and Extract Clozapine Compound Information
  • Query Chemical Identification Endpoints Use the preferred name
Task 2: Retrieve Mechanism of Action (MoA) and Human Targets
  • Query Drug Mechanism Endpoints
Task 3: Map Cross-Species Target Conservation
  • Execute Target Conservation Queries
Compound Information
https://ecodrugplus.helsinki.fi/api/v1/data/Compounds/preferred_name/Clozapine
Mechanism of Action
https://ecodrugplus.helsinki.fi/api/v1/data/DrugMechanism/preffred_name/Clozapine
Target conservation across the species

Example 1 :

https://ecodrugplus.helsinki.fi/api/v1/data/TargetConservation/organism/Homo sapiens/preffred_name/Clozapine

Example 2:

  • organism: Homo sapiens
  • target_species: Danio rerio
  • preffred_name: Clozapine
https://ecodrugplus.helsinki.fi/api/v1/data/TargetConservation/organism/Homo%20sapiens/target_species/Danio%20rerio/preffred_name/Clozapine

References

1. Haidary HA, Padhy RK. Clozapine. [Updated 2023 Nov 10]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2026 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK535399/
2. Shahid M, Walker GB, Zorn SH, Wong EH. Asenapine: a novel psychopharmacologic agent with a unique human receptor signature. J Psychopharmacol. 2009;23(1):65-73. doi:10.1177/0269881107082944
3. Knight AR, Misra A, Quirk K, et al. Pharmacological characterisation of the agonist radioligand binding site of 5-HT(2A), 5-HT(2B) and 5-HT(2C) receptors. Naunyn Schmiedebergs Arch Pharmacol. 2004;370(2):114-123. doi:10.1007/s00210-004-0951-4

EcoDrug+ developed in collaboration with the University of Helsinki and the University of Exeter.