One of the fundamental interests in the group is accelerated discovery of functional molecules from genetically-encoded libraries of chemicals. In these libraries, every chemical is linked to a bacteriophage that carries a unique genetic tag (see “Genetically-encoded fragment-based design” and “Genetically-encoded reaction discovery”). Similar approach enabled rapid discovery of molecules, which can be turned “on” and “off” using light irradiation (see “Chemical Optogenetics”). These unique molecular tools will be used to study the fundamental question in cell growth and differentiation (see “Forward Chemical Genetics and Cell Differentiation”). Our specific interest is asymmetric cell division of cancer stem cells and its role in tumor development and tumor treatment.
The translational areas of the lab are focused on development of portable platforms for detection of diseases in the developing world, and paper-based platforms for organic synthesis and biomolecular screening.
View Publications »
Access to billions of genetically-encoded molecules developed by our group allows solving the “impossible problems in molecular recognition”. One example of such unsolved problem is identification of ligands for “undruggable targets”: these are molecular receptors for which there are few or no therapeutics available. Proteins that recognize carbohydrates are one of the examples of such target. Protein-carbohydrate interactions are engaged in nearly all physiological responses, such as protein folding and degradation, cell-cell and cell-pathogen interaction, tumor growth and immune responses. Our group pioneered a powerful approach for genetically-encoded discovery of molecules that block or mimic protein-carbohydrate interactions (1,2). We currently use this approach to identify molecules that can be used as inhibitors of unwanted protein-carbohydrate interaction in drug-resistant tumors (via blocking of galectin-3 protein), development of cancer immunotherapy (by targeting DC-SIGN protein) and identification of improved molecular diagnostic for Tuberculosis (by targeting the TB-specific antibodies). We also expanded our genetically-encoded libraries to introduce arbitrary unnatural fragments (3) and develop general genetically-encoded fragment-based discovery of potent inhibitors and drug-targeting agents for other classes of undraggable targets. Examples are unique transmembrane receptors present in the blood-brain barrier and embryonic morphogen Nodal, which controls tumor growth.
1. S Ng, MR Jafari, W Matochko, R Derda* “Quantitative Synthesis of Genetically Encoded Glycopeptide Libraries Displayed on M13 Phage” ACS Chem. Biol., 2012, 7 (9), 1482–1487.
2. S. Ng, et al, “Genetically-encoded Fragment-based Discovery of Glycopeptide Ligands for Carbohydrate-binding Proteins“, J. Am. Chem. Soc. 2015, 137, 5248–5251
3. KF Tjhung, S. Ng, PI Kitov, EN Kitova, L Deng, JS Klassen, and R Derda* “Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries“, J. Am. Chem. Soc., 2016, 138, 32–35
Genetically-encoded libraries are one of the main sources for discovery of drug candidates in the pharmaceutical industry. Genetically-encoded libraries of peptides displayed on phage can be modified using bio-orthogonal chemical reactions to yield molecules with new function, improved stability or bioavailability. We are interested in identification of new chemical reactions that could modify unprotected peptides, in water, at an ambient temperature and physiological conditions (pH=4-10) to yield products with complex topology (macrocycles, bicycles, etc). Using these reactions, a chemical space of billions of peptides could be rapidly converted to a new chemical space, from which it is simple to identify valuable precursors to pharmaceuticals, vaccines, diagnostics, and materials. Some examples of synthesis of genetically-encoded libraries by our group are provided below:
1. S. Kalhor-Monfared, M. R. Jafari, J. T. Patterson, P. I. Kitov, J. J. Dwyer, J. J. Nuss and R. Derda “Rapid Biocompatible Macrocyclization of Peptides with Decafluoro-diphenylsulfone” Chem. Sci., 2016, 7, 3785-3790.
2. P Kitov, D F Vinals , S Ng , K F Tjhung , and R Derda “Rapid, Hydrolytically Stable Modification of Aldehyde-terminated Proteins and Phage Libraries”, J. Am. Chem. Soc., 2014, 136, 8149–8152.
3. S. Ng and R Derda* “Phage-displayed macrocyclic glycopeptide libraries” Org. Biomol. Chem., 2016, 14, 5539-5545
4. S Ng, MR Jafari, W Matochko, R Derda* “Quantitative Synthesis of Genetically Encoded Glycopeptide Libraries Displayed on M13 Phage” ACS Chem. Biol., 2012, 7
5. S Ng, MR Jafari, R Derda* “Bacteriophages and Viruses as a Support for Organic Synthesis and Combinatorial Chemistry“, ACS Chem. Biol. 7, 123.
Our Group develops technologies for activation or inhibition of specific proteins in specific location of of cell with the goal to control distribution of specific proteins during cell division, differentiation and asymmetric division. Our long term interest is to develop tools for “chemical optogenetics”, which is a field emerging on the interface of “chemical genetics” (interrogation of cell function using small-molecule inhibitors) and “optogenetics” (investigation of cell functions using proteins that can be reversibly activated by light). The main challenge is identification of potent light-responsive small-molecule ligands for a desired receptor in the cells. To address this challenge, we are developing genetic selections for ligands that can be reversibly activated or deactivated with light (1).
1. MR Jafari, Lu Deng, S Ng, W Matochko, K Tjhung, A Zeberof, A Elias, John S. Klassen, R Derda* “Discovery of light-responsive ligands through screening of light-responsive genetically-encoded library“, ACS Chem. Biol., 2014, 9, 443–450
M. R. Jafari, J. Lakusta, R. J. Lundgren, and R Derda* “Allene Functionalized Azobenzene Linker Enables Rapid and Light-Responsive Peptide Macrocyclization” Bioconj. Chem., 2016, DOI: 10.1021/acs.bioconjchem.6b00026
Our goal is to use unsupervised molecular discovery called “forward chemical genetics” to identify molecules and materials that can control differentiation and asymmetric division of cancer stem cells. These events govern tumor development through dynamic control of equilibrium between tumor-initiating cancer stem cells (CSC) and non-stem cancer cells (NSCC). Suppression of the emergence of CSC is critical for halting the growth and relapse of tumors. Large genetically-encoded libraries that contain >109 diverse molecules are uniquely poised for such discovery: by exposing the specific cell type, such as breast CSC, to a mixture of genetically encoded small molecules, we allow the cell to “select” all the molecules that bind to the cellular receptors present on the surface of CSC. This powerful approach requires no knowledge about the structure of composition of molecular receptors and it has the potential to provide all possible ligands for all cellular receptors at once. We couple this unsupervised discovery approach with ligand microarray technology developed by our group to accelerate the discovery of instructive materials that control differentiation of cancer cells to CSC.
1. F Deiss, W L Matochko, N Govindasamy, E Y Lin and R Derda “Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays”, Angewandte Chemie, 2014, 53, 6374–6377.
2. E. Lin, A. Sikhand, J. Wickware, Y. Hao and R Derda* “Peptide Microarray Patterning for Controlling and Monitoring Cell Growth” Acta Biomater., 2016, 34, 53–59
3. F. Deiss, Y. Yang, W. L. Matochko, R. Derda* “Heat-enhanced peptide synthesis on Teflon-patterned paper“, Org. Biolmol. Chem. 2016, 14, 5148-5156
Vast genetically encoded libraries are a powerful source of chemical information. Similarly to any large-scale information source (e.g., Internet), search in genetically-encoded libraries requires an efficient search engine; improper search approaches render such diversity useless. We hypothesize that the vast chemicals space of genetically-encoded libraries presently contains areas that cannot be accessed by conventional screens and we develop approaches that provided access to these “hidden ligands” (1). This process can be compared to internet search in “local network” (searching for the the results with the fastest connection) vs “global network” (searching for results regardless of the connection speed) or searching the Internet by biased engine such as Alta-Vista of 1990′s vs. searching the internet by unbiased (or less biased) search engine like Google engine of the modern days. One of the unsolved problem in molecular discovery is understanding the forces that govern genetically-encoded discovery; such knowledge allows development of molecular Google-like search engines for rapid, quantitative, reproducible and unbiased search in genetically-encoded libraries.
The key technology in our “search engines” is deep-sequencing (2), which can characterize hundreds of million of DNA sequences in a matter of hours. Other technology that empowers selection from genetically-encoded libraries builds on advances in microfluidics and micro-droplet technology (3). We demonstrated that handling of the libraries in micro-droplets (or micro emulsions) removes the unwanted biases in the selection landscape by isolating library members from one another and ceasing the unwanted competition between them (3,4). Genetically-encoded screens assisted by emulsion-amplification technology yield ligands that cannot be found in conventional screens providing one of the first examples of “improved search engines” in molecular discovery.
1. Derda R, Tang SKY, Li SC, Ng S, Matochko WL, Jafari MR. “Diversity of Phage-Displayed Libraries of Peptides During Panning and Amplification” Molecules 2011, 16, 1776-1803
2. W Matochko, K Chu, B Jin, SW Lee, G Whitesides, R Derda* “Deep sequencing analysis of phage libraries using Illumina“, Methods, 2012, 58 (1), 47–55
3. (a) Derda R, Tang SKY, Whitesides GM “Uniform Amplification of Phage with Different Growth Characteristics in Monodisperse Droplet-Based Compartments” Angew. Chem. Intl. Ed. 2010 49(31), 5301–5304; (b) Matochko, S Ng, MR Jafari, J Romaniuk, SKY Tang, R Derda* “Uniform amplification of phage display libraries in monodisperse emulsions“, Methods, 2012, 58 (1), 18-27; (c) K. F. Tjhung, S. Burnham, H. Anany, M. W. Griffiths and R. Derda “Rapid enumeration of phage in monodisperse emulsions“, Anal. Chem., 2014, 86, 5642–5648.
4. W Matochko, SC Li, SKY Tang, R Derda * “Prospective identification of parasite sequences in phage display screens“ Nuc. Acid. Res., 2014, 42, (3), 1784-1798.
The Derda group develops a variety of diagnostic platforms for the point-of-care detection of bacteria (1,2), antimicrobial susceptibility testing in portable culture devices (3), testing of drug-resistance of cells in 3D tumors models (4) or detection of disease biomarkers. (To showcase some of these technologies, we organized the first hands-on diagnostic workshop in Nairobi, Kenya in June 2012)
Our main platforms are paper-based devices that allow for culture of bacteria (1, 3) and human cells (4-6). The versatility and low cost of the portable devices for bacterial culture permits us to adapt standard assays performed in plastic Petri-dish into a compact, point-of-care format (1,3). Using three-dimensional models of human tumors (4, 5), we aim to develop patient-specific tests that could predict response of tumor to specific drug treatment.
We also use tools of molecular biology and synthetic biology to engineer “smart bacteriophages” that could recognize and respond to disease biomarkers, such as serological markers for tuberculosis (TB), and thus lead to TB detection using a cost-efficient antibody-free immunoassay.
1. MF Huacca, A Wu, E Szepesvari, P Rajendran, N Kwan-Wong, A Razgulin, Y Shen, J Kagira, R Campbell, R Derda* “Portable cultures for phage and bacteria made of paper and tape” Lab Chip, 2012, 12, 4269-4278. Lab on a Chip Top 10% article
2. R Derda, MR. Lockett, SKY Tang, RC Fuller, EJ Maxwell, B Breiten, CA Cuddemi, A Ozdogan, GM Whitesides “Filter-Based Assay for Escherichia coli in Aqueous Samples Using Bacteriophage-Based Amplification” Anal. Chem., 2013, DOI: 10.1021/ac400961b
3. F Deiss, MF Huacca, J Bal, K Tjhung, R Derda “Antimicrobial susceptibility assays in paper-based portable culture devices”, in review
4. F Deiss, A Mazzeo, E Hong, DE Ingber, R Derda,* GM Whitesides* “A Platform for High-Throughput Testing of the Effect of Soluble Compounds on 3D Cell Cultures” Anal. Chem., 2013, DOI: 10.1021/ac400161j
5. Derda R, Laromaine A, Mammoto A, Tang SKY, Mammoto T, Donald Ingber, Whitesides GM “Paper-Supported Three-Dimensional Cell Culture for Tissue-Based Bioassays” Proc. Natl. Acad. Sci. 2009, 106, 18457
6. Derda R, Tang SKY, Laromaine A, Mosadegh B, Hong E, Mwangi M, Mammoto A, Ingber DE, Whitesides GM “Multizone paper platform for 3D cell cultures“ PLoS One 2011, 6, e18940