Facilities

The Texas A&M Drug Discovery and Development Resource (3DRC) Center is a Texas A&M is a Texas A&M approved and regulated BSL2 facility that occupies approximately 7000 sq. ft. in the TMC3 Helix Park Collaborative Research Building, Texas Medical Center, Houston, Texas. It supports all stages of in silico, and in vitro preclinical drug discovery and development and is well-equipped to perform virtual screening, medicinal chemistry, high throughput screening, and data analysis in this proposal. The core provides industry-standard computational resources, synthetic chemistry, liquid handling, and high throughput end-point detection capabilities for scientists carrying out chemical, chemical-genomic, and drug discovery research and can support biochemical, cell-based, and foundational organism library screens. In addition to traditional high throughput screening, our facility supports the development of specialized capabilities for lower throughput drug discovery and development needs, such as optical metabolic imaging, microelectrode array and impedance systems for discovery and toxicity testing, and spectral flow for high complex multiplex biomarker development and testing.

Drug Libraries

A detailed description of drug libraries can be found here. A complete list of all (active and previously offered) drug libraries can be viewed and downloaded here

Equipment

Synthetic Chemistry

The newly established synthetic chemistry laboratory is equipped with state-of-the-art instrumentation that enables rapid compound synthesis, purification, and characterization essential for advanced research projects. The laboratory features six 8-foot chemical fume hoods with appropriate glassware and scaffolding to ensuring safe handling of chemicals during synthesis. For purification processes, the laboratory houses a Buchi Prep C-830 preparative HPLC system capable of chiral separations us-ing chiral columns, and a Biotage Isolera One flash chromatography instrument for automated purification of reaction mixtures. Solvent removal and sample concentration are efficiently managed using three Buchi Rota-vapor R-300 rotary evaporators with F-305 recirculating chillers. A Labconco FreeZone 2.5 L -50°C benchtop lyophilizer provides freeze-drying capabilities for peptides and small molecules. Analytical characterization is supported by a Shimadzu LC-MS system with a mass spectrometry detector, enabling compound characterization and real-time reaction monitoring. A Bruker Fourier 80 benchtop NMR spectrometer with 1H and 13C probes offers capabilities for both one-dimensional and two-dimensional NMR studies, essential for structural elucidation. The laboratory also includes a Mettler Toledo Karl Fischer titrator for accurate moisture analysis and two Mettler Toledo analytical balances for precise weighing of reagents. Additional equipment includes two biosafety cabinets for handling sensitive materials and ensuring a contamination-free environment, as well as a VWR ultrasonic sonicator for efficient sample preparation. An automated peptide synthesizer facilitates efficient and precise peptide assembly, while parallel block reactors and curated structure-activity relationship (SAR) kits from Sigma-Aldrich allow for expedited synthesis and diversification of compounds, accelerating SAR studies and the development of in silico hits. This comprehensive suite of advanced instrumentation positions the laboratory to effectively support high-level synthetic chemistry research, promoting innovation and accelerating the development of novel compounds.

Automated high-throughput screening platforms

The CDDP maintains and operates two automation platforms for setting up in vitro HTS assays. The primary screening system is built around a Labcyte Echo 550 acoustic dispenser. The Echo is a ‘No-Touch’ acoustic energy dispensing device where there is no physical contact during the transfer of compounds from a source to an assay plate. A Labcyte Access integration platform automates plate handling between the Echo and other integrating devices. The Access platform automates plate transfers between a Thermo Cytomat 6000A automated cell culture incubator with a capacity of 189 multi-well plates, a Thermo Multidrop Combi and the Echo. The second HTS platform used by the CDDP is a Tecan Freedom Evo 200. The Evo platform has a variable spanning 8-channel LiHa liquid handling arm, a robotic manipulator arm and an interchangeable 96/384 multichannel or pin tool liquid handling arm. This workstation is also fully integrated and designed to perform both cell-based and biochemical assays in a wide variety of configurations from single tubes to 384-well microplates. Integrated onto this Tecan platform are Liconic robotic incubators for both room temperature storage of reagents and consumables and a temperature, humidity and CO2-controlled cell culture each capable of housing up to 210 multiwell plates. Additional inte-grated peripherals include a Tecan Hydrospeed plate washer, a Thermo Fisher Multidrop bulk liquid dispenser, an Agilent V-spin plate centrifuge and a Tecan Infinite M1000pro multifunction reader.

Automated high-throughput microscopy platforms

The CDDP maintains and operates three automated microscope platforms from General Electric Healthcare and Molecular Devices for performing in vitro HTM assays. Our primary platform for fixed cell analysis is the GE Healthcare IN Cell Analyzer 6000, a high-performance, laser-based confocal imaging platform featuring a novel and proprietary optical system that incorporates an iris-like variable aperture design for adjustable confocal imaging and 16-bit sCMOS scientific camera. The system is equipped with objectives covering low 4x/0.20NA magnification to high 40x/0.95NA magnification. Multiplex fluorescent assays of up to four different colors can be simultaneously captured. The addition of a four-axis cylindrical coordinate microplate arm and scheduling software enables unattended image collection for up to 35,000 wells per day. The primary platform for three-dimensional model systems is an au-tomated Molecular Devices ImageXpress Confocal HT.ai Imaging System configured with two selectable con-focal disk geometries and internal environmental control of both humidity and CO2 for extended imaging capabilities. This ImageExpress has been optimized for the high-capacity screening of both organoids/spheroids and microphysiological systems (tissue chips) through its 7-channel high-intensity laser light source with up to eight imaging channels to enable multiplexed live cell assays while maintaining high throughput by using short-ened exposure times and a water immersion objective that improves image resolution, minimizes aberrations, and increases imaging deeper into 3D structures. This particular automated platform uses a PF400 collaborative arm to integrate the ImageXpress seamlessly with a Liconic Wave cell culture incubator (37ºC, 95% RH, 5% CO2) suitable to support standard live and with integrated room temperature storage for fixed cell imaging, but more importantly, the Wave incubator is suitable to support the high throughput tissue chips built on the Mimetas microflow platform with a built-in rocking capability to enable microflow on those plates. The CDDP also has an automated ImageXpress Confocal Micro platform that is a high-performance system with solid-state light sources. This ImageExpress confocal microscope platform are configured with two selectable con-focal disk geometries and internal environmental control of both humidity and CO2 for extended imaging capa-bilities. Images are collected using a 16-bit sCMOS sensors with fast acquisition times that helps preserve specimens. As with the IN Cell Analyzer 6000, the ImageXpress enables one to optimize for both speed and image quality with software selectable objectives covering low 2x/0.10NA magnification for ultra-high throughput of nearly 200,000 images/day to high 40x/0.95NA magnification for higher content imaging all on the same platform. The software also allows one to change from confocal imaging mode to wide field-of-view mode without the need of manually reconfiguring the system. Thus, the plates same can be imaged using both modes sequentially. Multiplex fluorescent assays of up to five different colors can be simultaneously captured. The sys-tem is also capable of capturing FRET-based reporters. These automated microscope platforms also have au-tomated cell culture incubators optimized for long-term live cell imaging, bulk liquid dispensors for reagent addition, and arms to move plates to and from the microscopes and other integrated devices.

Automated Optical Metabolic Imaging

Changes in cellular metabolism have long been recognized as a fundamental feature, and are now considered a hallmark, of cancer. The CDDP employs an ad-vanced two-photon fluorescent lifetime microscopy metabolic imaging method to significantly enhance our un-derstanding of how specific microenvironmental factors influence the regulation of cancer cell metabolism and drug responsiveness at a single cell level. This platform uses a noninvasive, quantitative measure of the intrin-sic fluorescence of reduced nicotinamide adenine dinucleotide (NADH) as a natural biomarker that is involved in many important cellular processes including mitochondrial function, energy metabolism, calcium homeostasis, gene expression, oxidative stress, aging, and apoptosis. This platform also measures the autofluorescence of flavin adenine dinucleotide (FAD) that is localized in the mitochondria and is involved in the TCA cycle and complex II in the electron transport chain. The CDDP platform is from Intelligent Imaging Innovations (3i) and employs femtosecond laser pulses (680-1080 nm, 140 fs, 76 MHz) generated using Chameleon Ultra II Ti:Sapphire Laser system (Thorlabs Inc., Newton, NJ). The laser pulses were steered toward dual channel time-correlated single photon counting (TCSPC) electronics and an inverted microscope (Zeiss Axio Observer Z1 fully motorized inverted microscope) fitted with environmental controls for temperature, humidity, and CO2. The platform has a motorized X,Y stage with 0.1µm linear encoders to support the use of either slides or multi-well plates (96-384well/plate). This platform is equipped for both live and fixed cell widefield epifluores-cence applications, transmitted illumination, and multi-photon techniques.

Analytical microscopes

Several conventional high content imaging systems are available in the CDDP. For high content 3-D imaging or where oil-immersion is preferred, the CDDP uses a Nikon W1 Yokagawa spinning disk confocal or a General Electric Healthcare DeltaVision Elite deconvolution micro-scope. Both of these platforms feature climate controlled (temperature, humidity, CO2) automated stages which provide a large range of live cell capabilities. The both microscopes have multidimensional acquisition (x,y,z, wavelength, time), up to 5 channels (fluorescence and brightfield/DIC), FRET, multi-point acquisition, large area acquisition (tiling), dual Autofocus (Hardware & contrast based), fast acquisition mode and 4x,10x,20x,40x air, 40x Oil, 60x oil, 100x oil objectives.

Automated flow cytometry

For multiplex high throughput screening of nonadherent cell-based models, the core uses an automated flow cytometry platform. The heart of the platform is a 5 laser, 30 detector BioRad ZE5 high throughput flow cytometer capable of running uninterrupted for up to 20hrs. The flow cytome-ter is integrated with an integrated robotics workstation that provides a structure to hold all equipment in a fixed orientation around an articulating Universal Robotics 6-axis UR10 robotic plate manipulator. The platform also includes integrated peripheral devices to automate most experimental procedures needed for routine flow analysis. This equipment includes an automated cell culture incubator, a refrigerated incubator to hold plates at 4ºC for extended periods of time, an on-deck automated centrifuge, a deep-well plate washer, a multi-reagent bulk liquid dispenser and plate shaker, a Formulatrix Mantis automated microfluidic dispenser, a microplate reading bar code scanner, and a room temperature storage and delidding device. All of the scheduling and integration is handled using Hudson Robotic’s Softlinx software.

Computing resources

3DRC maintains a network of computational workstations and servers collectively functioning as a distributed grid computing cluster. In total, this network provides more than 400 CPU cores and over 4 TB of high-speed RAM, providing ample computational power for a wide range of image analysis and conventional data modeling techniques. Other critical features include multiple specialized high-capacity GPU compute nodes with one containing four NVIDIA A6000 Ada 48Gb GPUS, seven containing dual NVIDIA RTX A6000/48Gb with SLI, one with a single NVIDIA RTX A6000/48Gb and one with a NVIDIA Tesla V100 (32GB), similarly providing ample resources for training and deploying deep learning driven workflows. The core laboratory also maintains a centralized image and data repository of more than 700TB with a redundant mirrored backup system maintained by the Texas A&M Office of Information Technology in College Station, TX. Multiple software are used to support drug design and cheminformatics, including PharmacoNet, DiffDock, GNINA, Vina, QuickVina, ChimeraX, BioVia Draw, KNIME, and Pipeline Pi-lot. Multiple generative open-source generative ligand design software have been implemented and include dragonfly, polygon, synthemol, SPMM, and drugGPT. New methods are continually assessed and encorperat-ed as needed. Data analysis from in vitro biochemical and cell-based assays is performed using a combination of Pipeline Pilot from Biovia, Microsoft Office 365, R, Python, and GraphPad Prism. High-content image analy-sis algorithms are developed and executed using the IN-Cell Developer, MetaXpress Analysis (Molecular De-vices), or Pipeline Pilot (Biovia). Deep learning models are developed and trained in either Pipeline Pilot (Bio-via), or in Python/Pytorch. Virtualization software includes WSL2 and Docker. Operating systems include Win-dows 11, Windows Server 2022, Ubuntu 22.04, and Red Hat Enterprise Linux. Additional software include Mi-crosoft 365 Suite, Adobe CC Suite, Graphpad Prism, FlowJo. Additional computational resources are made available to all Texas A&M faculty and staff through the HPRC resource center (https://hprc.tamu.edu/) and cloud computing resources.

Research Network

The Gulf Coast Consortium for Innovative Drug Discovery and Development

The Consortium for Inno-vative Drug Discovery and Development (GCC IDDD) is a research consortium formed in 2003 that is focused on providing support for Houston/Galveston scientists in advancing their therapeutics discoveries through de-velopment to the clinic. Consortium support includes collaborative networking and joint funding opportunities, shared core resources, and educational programs. Drs. Stephan and Powell is an active member of the IDDD Executive Steering Committee.

The CPRIT Cancer Therapeutics Training Program

The Cancer Therapeutics Training Program (CTTP) is a multi-institutional post-doctoral training program funded by the CPRIT and is designed to prepare post-doctoral trainees for future careers in academic and/or commercial cancer therapeutics research and develop-ment. The goal of the program is to recruit and train scientists equipped with the essential skills and knowledge necessary to translate basic cancer research discoveries into commercially viable cancer therapeutics. Drs. Stephan and Powell are a faculty member of the CTTP, a co-mentor to participants, and a member of the applicant review committee.