Established in 2006, the University of Pittsburgh Drug Discovery Institute (UPDDI) combines the expertise of faculty from the School of Medicine, School of Arts and Sciences, School of Pharmacy, and Graduate School of Public Health in pursuit of a common goal: to identify small molecules that will ultimately result in drug therapy treatments for orphan and neglected diseases as well as other diseases. The Institute, housed in the new Biomedical Sciences Tower 3 (BST3), operates the Pittsburgh Molecular Libraries Screening Center, one of 10 NIH-funded centers providing public access to robust, sensitive, rapid, and cost-effective assays capable of screening a wide range of molecular targets against hundreds of thousands of existing and novel compounds. This year UPDDI members received $38M in extramural grant support with over $8M being administered by the UPDDI administrative staff.

With the completion of our planning, building, prioritizing and moving phases, the UPDDI is now focusing its full attention on our core mission and goals.

The Mission Statement of the UPDDI

• Expand the use of high-throughput screening and high-content screening for orphan disease-related drug discovery at the University of Pittsburgh


• Enhance the strengths and interactions among the Schools at the University of Pittsburgh


• Train the next generation of drug discovery investigators

• Assist faculty and students with the development and implementation of robust HTC/HCS assays


• Recruit assays from faculty and cultivate external HTS/HCS projects


• Disseminate information concerning compound activity


• Assist faculty and students with lead compound optimization


• Educate the public about drug discovery process


• Be inclusive and multi-disciplinary by actively recruiting members from all school and academic units at the University of Pittsburgh


• Provide the University of Pittsburgh with access to HTS and DOS facilities with multiple robotic platforms and more than 280,000 small molecules, marine and plant extracts


• Increase extramural funding for the Institute

The screening data workflow of UPDDI includes compound registration, compound inventory, compound transfer, assay design, assay detection, screening data view and quality control, hits detection, SAR and PubChem data report. The two flowchart pictures depict the HTS and secondary screening data workflows.

The UPDDI Screening Facility, located on the 9th and 10th floors in the Biomedical Science Tower 3, provides investigators with the ability to run High Throughput and High Content Screens. The following equipment and resources are available for investigators:

At the UPDDI, the LIMS (Laboratory Information Management System) software is being deployed and implemented to manage the work flow among the compound storage and retrieval, compound transfer, compound cherry picking, assay design, screening detection, screening quality control, hit detection, SAR report and PubChem screening data publication.

Also, the Electronic Laboratory Notebook will be deployed to provide the scientists with a single access point for capturing experimental data and performing scientific tasks.

High-throughput screening has become the dominant tool in the drug discovery process. In its earliest form, drug screening typically involved antimicrobial formats. However, rapid progress in the fields of genomics, proteomics and molecular biology has expanded the target landscape beyond microbial targets, to both increase the numbers of potential drug targets, and facilitate development of assays to screen these targets. In parallel with these changes, developments in robotics and combinatorial chemical synthesis have driven the production of very large numbers of compounds with potential for pharmacological activity. The need to screen large libraries of chemical compounds against multiple targets has stimulated improvements in assay technology, instrumentation, and automation that evolved into the field of HTS and has revolutionized the field of drug discovery. In recent years, advances in miniaturization, parallel processing and data management have enhanced efficiency by controlling costs and increasing throughput thereby supporting the evolution of multiple platforms for lead generation.

Upon selection of a target, a lead generation strategy is defined which typically includes HTS as the first step – the “primary” assay, followed by hit confirmation – “secondary” assays, which precede lead validation and optimization. Many factors can influence the format of the assays employed and their positioning in the screening paradigm; the type of pharmacological information sought, the target class, throughput, cost, and other logistical or practical considerations. Cell based screens and biochemical or isolated target screens each have their merits. Biochemical assays which utilize isolated enzymes, proteins or receptor preparations are generally amenable to homogeneous assay formats and miniaturization, potentially identify the majority of chemotypes that interact with the target, and can provide target specificity information. In contrast, issues like cell membrane permeability and compound cytotoxicity may limit the diversity of chemotypes and pharmacophoric information obtained from cell based screens, and cellular assays are more challenging to miniaturize or automate.

The purpose of HTS is the interrogation of large chemical collections in the context of a biological target to accurately identify active chemotypes. To achieve this purpose, screens must be configured to provide a robust, reproducible signal with adequate throughput to screen large compound libraries. Since the activity or inactivity of any given compound in an HTS will typically be determined in a single well at one concentration, the assay signal window (dynamic range) must be sufficiently rugged to provide adequate separation between the maximum and minimum responses, and should enable the response to active compounds to be discriminated from the background variability (noise) associated with the top and bottom of the signal window. In addition to studies designed to validate the kinetics and pharmacology of the assay, efforts are made to optimize the signal window and/or variability of the assay in the context of a number of variables dictated by the automated process; DMSO tolerance, reagent stability, and signal stability. Superimposed upon assay development parameters associated with biochemical HTS formats, the implementation of cell-based screens present additional challenges; generation and/or characterization of an appropriate cell model, production of sufficient cells for HTS, plating cells for the assay, effects of compound exposure, and capture of the assay signal.

High-content Screening (HCS) is an extension of a revolution in cell analysis that began about 3 decades ago when fluorescence labeling technologies were combined with electronic imaging technologies and used to study individual cells on a light microscope. The innovation that drove the development of HCS, and what distinguishes HCS systems from the many confocal and wide field microscopes, is the integration and automation of the entire analytical process. The first HCS platforms were introduced to the drug discovery market by Cellomics, Inc. (Pittsburgh, PA) starting in 1997. There are now more than ten models of HCS imagers established in the market. HCS platforms automate the capture and analysis of fluorescent images of millions of individual cells in tens of thousands of samples on a daily basis, and have made fluorescence microscopy and image analysis compatible with the needs of drug discovery and systems cell biology. Through selection of appropriate probes, antibodies, fluorescent protein fusion partners, biosensors, environmentally sensitive probes and stains, fluorescence microscopy can be applied to many drug target classes, may be configured for simultaneous multiple target readouts (multiplexing), and can provide information on distributions and cell morphology in addition to simple intensities. Image based assays therefore provide multi-parameter quantitative and qualitative information beyond the single parameter target data typical of most other assay formats, and thus are referred to as high “content” assays. In recent years there has been a growing trend in drug discovery towards the implementation of cell based assays where the target is screened in a more physiological context than in biochemical assays of isolated targets. Fluorescence microscopy, whether confocal or wide field, is one of the most powerful tools that cell biologists can use to interrogate bio-molecules and investigate the molecular mechanisms of the cell. Automated imaging platforms are therefore being deployed throughout the drug discovery process; target identification/target validation, primary screening and lead generation, hit characterization, lead optimization, toxicology, bio-marker development and diagnostic histopathology. Furthermore, these platforms are now spreading into the research markets for application in high throughput biology.

The UPDDI supports three main databases: a cheminformatics database, an image storage and analysis database and an Electronic Laboratory Notebook (ELN) database.

The UPDDI has a Matrical MatriMinistore Modular Compound Store platform, which is integrated with the LIMS to manage the compound storage and retrieval. This platform features: