At MTP, we focus on working together to create and adapt cutting-edge biomolecular screening technologies. These technologies help us discover compounds that can selectively interact with or modify the functions of specific molecular targets important to the CCR, NCI. These compounds, which can be non-peptidic, peptidic, or protein-based, are used as "bioprobes" for target validation research or as leads for drug discovery. Here are some collaborative research opportunities available with us::
In the past decade, biomolecular screening technology has advanced rapidly, driven by combinatorial chemistry, diverse chemical sources, and developments in genomics and proteomics. This field has become crucial for molecular target research, validation, drug discovery, and development.
A key challenge in discovery projects is creating a practical and valid assay model for primary screening of chemical libraries. An ideal model must work well with high-throughput screening (HTS) platforms and include complementary secondary assays for further evaluation.
Assay models for primary or secondary screening may include receptor binding, immunoassays, enzyme assays, interactions between proteins, nucleic acids, carbohydrates, gene expression, or functional assays. Common detection methods are luminescent, fluorescent, or colorimetric. These models can be cell-based or biochemical and either homogeneous or heterogeneous.
To adapt assays for high-throughput screening (HTS) of chemical diversity, we often need to modify standard lab tests while keeping their core biology. For HTS, we need to consider cost, speed, and robustness, which means substantial changes to lab assays without loss of the essential biology. This includes adapting to robotic liquid handling and specific detection methods like time-resolved fluorescence. We work collaboratively with intramural project advocates to make these modifications.
The MTP continuously improves the hardware, software, and biological capabilities for HTS applications within the CCR, NCI. Besides using commercial chemical diversity sources, MTP and collaborators can screen non-discreet compound collections from NCI repositories under the NCI Developmental Therapeutics Program. Additional sources for MTP research include Display Technologies and Natural Products, particularly the NCI Natural Products Repository, a unique and valuable resource for targeted discovery research. Other compound libraries to be assayed may comprise of synthetic or natural compounds, or a mix thereof, some of which may be available from many commercial suppliers.
In addition to the intramural community of world-class scientists comprising the CCR, there are other unique resources available at the NCI that provide extraordinary opportunities for intramural collaborations in molecular target elucidation, validation and drug discovery research.
Such a resource is the NCI Natural Products Repository (NPR), which contains the largest and most diverse natural products extracts collection in the world. The NPR collection is derived from more than 15 years of NCI contracts-based collections programs led by renowned botanical, marine science and microbial research professionals and organizations globally. The NPR resource is available to NCI/NIH intramural scientists, as well as qualified extramural scientists and organizations, subject to institutional policies, procedures, and constraints described in detail elsewhere.
Each of the nearly 150,000 unique samples residing in the NPR comprises many thousands of individual compounds in a complex aqueous or organic solvent extract matrix. Effectively, the total chemical diversity residing in the NPR equates to tens to hundreds of millions, if not billions of different, often very complex, structures. This provides a rich resource for discovery of novel research probes for molecular target manipulation, and new potential leads for drug discovery research and development. However, the isolation, purification, and structural elucidation of these unique leads from such complex extracts requires highly specialized skills and technologies. MTP scientists have extensive experience in developing and applying bioassays and high-throughput technologies tailored for prioritization bioassay-guided fractionation, purification and characterization of novel lead molecules from natural product extracts.
The MTP invites proposals from CCR intramural investigators for collaborative research on molecularly targeted lead-discovery research of natural products. The MTP may also consider collaborative projects for molecularly targeted lead-discovery from natural product extracts or collections originating from selected collaborating researchers or organizations other than from the NPR. In such cases, collaborative projects are considered based both upon unique and mutual scientific drug discovery and development interests and resources of the collaborating parties.
The MTP is interested in collaborating with external groups to acquire broader chemical diversity for screening in our high throughput screens. Please consult our guidelines for information on the types of samples that are of interest to the MTP.
Guidelines for MTP Chemical Libraries
1.0 Desired samples
The Molecular Targets Program (MTP) maintains a large chemical library of pure compounds and natural product extracts for screening in high throughput assays related to cancer and viral disease. Our mission includes discovery of both drug leads and chemical probes. We welcome samples from collaborators which increase the chemical diversity of our screening collection. Our focus is on natural products and natural product-like synthetic compounds. We generally do not purchase screening samples; instead, we rely on collaborations where testing data is traded for access to screening samples.
1.1 Pure Compounds
We particularly value chemical diversity from natural sources and diversity-oriented synthesis. Preferred features include chirality, extensive functionalization, and lack of reactivity. Planar, aromatic combinatorial libraries, and compounds with reactive functional groups are not our focus. Compounds need not conform to Lipinski’s rules of five, however we prefer to avoid polyphenolics and other “nuisance” compounds.
1.2 Extracts
Current areas of interest include extracts of high altitude plants, unusual fungi, central Asian plants, temperate marine invertebrates, and plants used as spices or condiments. As extracts from many tropical plants and Pacific marine invertebrates are currently well represented in our collection, extracts from these sources will not be a priority. Our current preference is to process 100-200 mg amounts of extract through a prefractionation process, generating multiple samples per parent extract. These fractions are used for screening.
2.0 Mechanism for collaboration
The MTP prefers to work with library source organizations under a formal Material Transfer Agreement (MTA) which defines the rights and responsibilities of the MTP and the source organization. A draft agreement is generally modified to fit specific needs of both organizations. The NCI Technology Transfer Center assists in developing MTAs and other agreements.
3.0 Desired sample data
3.1 Pure Compounds
We require the chemical structure of all submitted compounds be supplied prior to testing. The structures will be held in confidence. These structures should be submitted in the sd file format with unique compound identifiers. Use of laboratory notebook identifiers as primary identifiers is discouraged. In addition to the sd file, a spreadsheet containing all relevant data is required. For samples submitted in 2D-bar coded vials or plates, the rack or well locations must be specified completely. Molecular formulae and molecular weight data are also useful, and while these can be calculated from the structure, adding them to the spreadsheet can serve as an internal check of the correctness of the structure. Compounds should be at least 90% pure, as judged by NMR, HPLC, or other methods. We do not require detailed QC data to be supplied to us prior to screening, nor will we routinely conduct QC studies of screening compounds.
3.2 Extracts
Source taxonomy is requested. In some cases (microbes) this may not initially be feasible, but for most samples it is enormously helpful in prioritizing extracts for bioassay-guided fractionation.
4.0 Desired sample format and amount
Our most favored sample format is 1.4 mL 2D bar coded polypropylene tubes in 96-position racks (preferably Micronic). It is usually most convenient to ship the samples dry. Either 0.5 mg or 1.0 mg amounts are sufficient for screening purposes. We would prefer that source organizations not ship larger amounts of screening compounds. Less favored formats are ordinary polypropylene or glass vials, 96-well plated compounds, and non-bar coded tubes. Bar codes should be used to identify samples if at all possible with any format. For extracts, our prefractionation process requires 100-200 mg of extract, depending on type of extract. If prefractionation is not to be done, 5.0 mg of extract is sufficient for obtaining primary screening results. All samples should be accurately weighed prior to shipping, or aliquotted and evaporated from solutions of known concentration. Samples will routinely be dissolved in DMSO after receipt and stored frozen at -20°C.
5.0 Resupply of pure compounds
Once active samples are identified in HTS assays and confirmed, it is our practice to request a fresh sample from the supplier for dose-response studies, secondary in vitro screening, and confirmation of sample identity and integrity. Given that hit rates for most of our HTS assays are less than 1%, it is our experience that most source libraries do not provide hits in all assays. Nonetheless providers should have a plan for resupplying active samples and should verify the quality of the sample at the time of resupply.
6.0 Analog synthesis
At the same time as resupply of hits is requested for synthetic compounds, we often request any structurally related compounds the provider may possess, in order to develop structure-activity relationships around the hit. Note that we do not have an efficient means of funding analog synthesis at this time, although NIH grant supplements can serve this purpose.
7.0 Coordination with NCI collaborators
All assays run by the MTP are developed in collaboration with one or more NCI Intramural Principal Investigators (PI). The PI is generally an expert in the biology which the assay attempts to address, and is usually heavily involved in secondary evaluation of initial hit samples. The PI is almost always involved in patent filings and publications as a collaborator, co-inventor, and co-author.
8.0 Publications and Patents
For those active compounds that survive secondary evaluation and are judged of sufficient biological interest, patents and/or publications are likely. Scientists from the source organization will be included in inventorship and authorship. This is more fully detailed in the MTA.
9.0 Data return to source organization
Suppliers will be notified of confirmed hits as they emerge from the screening campaign. In addition, full testing data for all supplier compounds will be communicated to the supplier on a semi-annual basis. Each set of assay results will include contextual information about the nature of the screening assay, criteria for hits, and biological relevance. We typically run three or four HTS campaigns per year. Every supplier library may not be run in every HTS assay due to assay cost considerations or assay robustness issues. It is helpful to have a single designated point of contact at the supplier organization for communication about hits, resupply and data return.
The MTP welcomes opportunities to assist in the development or application of other pertinent discovery tools, which might include more specialized bioassays, screens, reagents or related technology of interest to CCR investigators.
The MTP is eager to collaborate in the evaluation or implementation of a broad range of available or evolving "discovery" and validation technologies, including proprietary methods, hardware, software, compounds or collections, from the private-sector. In so doing, the MTP intends to enhance the CCR's intramural capabilities for follow-up investigations of screening hits, bioprobe or drug-lead discovery and characterization, identification and validation of new molecular targets, and other pertinent research supporting preclinical or clinical advancement of molecular therapeutics, diagnostics and imaging.