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Computational and Medicinal Chemistry

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The Purdue University Center for Cancer Research (PCCR) has acquired both external (the Walther Cancer Foundation and the Indiana Clinical and Translational Sciences Institute) and internal funds (non-CCSG) to establish this new Resource. The development of the Computational and Medicinal Chemistry Shared Resource (CMC-SR) will expand the probe development and drug discovery services available to both PCCR members and the Purdue University research community - services that have not been routinely available prior to 2012. The CMC-SR will provide a crucial and previously “missing link’ between the Biomolecular Screening services offered by Bindley Biosciences Center and PCCR’s Biological Evaluation Shared Resource (BE-SR).

The primary mission of the CMC-SR is to accelerate the development of molecular probes and small molecule therapeutics for Center members. Some PCCR members requested synthesis of molecules that would serve as probes of biological function to validate their targets in conjunction with siRNA etc.; other members requested the design and synthesis of compounds against their targets with the desire to develop anti-cancer therapeutics. In response, the CMC-SR will offer services and collaboration in the following areas: (1) in silico screening of compounds libraries, (2) advanced cheminformatics analysis on primary high-throughput screening (HTS) hit data, (3) computational docking studies and analyses, (4) structure-based design of molecules, and (5) synthetic medicinal chemistry services to optimize lead compounds for biological evaluation. The CMC-SR Scientific Advisory Group, which utilizes a project coordinator who will be assigned to members’ projects, will shepherd Center members through the process (Figure 1). PCCR’s Drug Evaluation Committee, which serves to evaluate projects most meritorious for advanced pre-clinical development to the point of investigational new drugs (IND) and Phase 0/1 clinical trials, will guide and provide advice to the CMC-SR Scientific Advisory Group.


  • Dual Channel Automated Flash Chromatography System: Smart Flash EPCLC W-Prep 2XY, Yamazen

  • Rotavapors: Buchi R 215 with Neslab RTE 7 chillers

  • Microwave Reactor: CEM Discover SP

  • Analytical Balance: Mettler Toledo XS 204

  • HPLC Agilent 1200 with fraction collector

Services & Pricing

The CMC-SR will provide an array of support services spanning from in silico screening, to synthetic medicinal chemistry optimization of lead compounds with advanced ADMET properties designed into the molecules. Details on the specific services offered are provided below.

Call for a cost estimate. In Silico Screening Services

This service supports computer-based, virtual screening of both in-house (~220K compounds) and external compound collections, through docking and other computational and modeling approaches. In concert with cheminformatics approaches, bioassay data are analyzed to propose likely binding arrangements and 3D pharmacophore maps. Computational docking can be performed using available X-ray, NMR or homology models of protein structures of interest. If needed, homology models can also be generated and validated using structure-activity-relationship (SAR) correlations coupled with computational docking approaches. Structure-guided and combinatorial compound generation tools are used for hit-to-lead optimizations.

Services include 3D pharmacophore modeling and screening, homology modeling, high-throughput virtual screening of in-house and external libraries, and comparison of in-house libraries for hit density and structure-based design of novel drug candidates. The majority of the computational modeling workflow is accomplished via the Schrödinger program suite (LigPrep, Glide, CombiGlide, and Prime).

Cheminformatics Support Services

The Cheminformatics service supports compound management (registration, inventory, plate formatting and tracking), processing, analysis of HTS data, and data mining using both local and public databases. The Cheminformatics service also supports SAR analysis of bioassay results and, in conjunction with computational modeling approaches, can propose likely binding arrangements of HTS hits and 3D pharmacophore maps. The 2D and 3D SAR results can be further utilized in small-molecule design for custom synthesis or commercial acquisition of follow-up compounds. Services include:

  • HTS data processing, analysis, and secure sharing of results across assays and investigators
  • Database mining
  • SAR analysis and development by integrated cheminformatics and docking approaches
  • Design of follow-up compounds or libraries
  • Identification of commercial sources for compounds of interest and their analogs
  • Screening data management, which allows creation, capture, analysis and storage of chemical, biological and ad hoc research data
  • Prediction of pKa values and tautomerism in putative ligands using the robust tool, Epik
  • Prediction of ADME properties of drug candidates using QikProp.

The majority of the cheminformatics workflow is accomplished via the Dotmatics (Browser, Vortex, Pinpoint, Nucleus, Register, Studies) program suite. This fully integrated, web-based cheminformatics platform automates data processing from the compound information (structure, plate location, etc.) and assay results, to the HTS data analysis, compound clustering and SAR exploration. An Oracle database, maintained by Information Technology at Purdue University (ITaP), is utilized for Dotmatics data management. In addition, Schrödinger’s Epik and QikProp programs are used to predict ADME properties in hit-to-lead optimizations.

Compound Libraries Available

The current compound collection of approximately 220,000 unique entities has been assembled from commercial (ChemBridge, Asinex, ASDI and LifeChemicals) and synthetic libraries provided by on- and off-campus researchers. The current collection is composed of mostly drug-like compounds, supplemented with natural products and synthetic intermediates.

Medicinal Chemistry Support Services

The medicinal chemistry component of the CMC-SR was established in November 2013 to provide synthesis of small molecule compounds that support probe development, drug discovery, and development projects of PCCR researchers. The medicinal chemistry component works closely with the computational chemistry component of this Shared Resource and with the Biomolecular Screening facility in Bindley Biosciences Center. Services include:

  • Triage of high-throughput screening (HTS) data for the selection and follow-up of promising leads
  • Development of novel or streamlined synthetic strategies for desired molecule(s)
  • Synthesis of substrate or probe molecules for high-throughput screening applications.
  • Small-scale synthesis (1 - 100 mg) of lead-like, drug-like and diagnostic probe-like molecules
  • Lead-compound analog expansion for improvement of potency
  • Improvement of ADMET (adsorption, distribution, metabolism, excretion, toxicity) properties of lead compounds while maintaining or improving activity
through medicinal chemistry approaches
  • Patentability assessment of chemical matter

Contact Information & Location

        • Medicinal Chemistry Leader: Antonella Pepe, Ph.D.
        • Email:
        • Phone: (765) 496 - 1687
        • Building/Room: DRUG 111

      • Computational Chemistry Leader: TBA
      • Email:
      • Phone: (765) 494 - 7249
      • Building/Room: HOCK 218
  • Computational and Medicinal Chemistry Shared Resource Hockmeyer and Bindley

  • Purdue University Center for Cancer Research
    Hansen Life Sciences Research Building
    201 S. University Street
    West Lafayette, IN 47907-2064

  • Phone: (765) 494-9129
    Fax: (765) 494-9193
    Contact us with questions at:

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