The Zondlo Research Group

Laboratory of Organic Chemistry

and Molecular Design

Current Research

Our research focuses on the design, synthesis and development of small molecules and minimalist polymers with biological activity, the elucidation of fundamental principles of and discovery of effectors of biological interactions, the development of novel, functional proteins, and the development of novel and useful methods of enantioselective catalysis.

Our interests center on the general area of functional molecular recognition: the generation of novel molecular structures and architectures which interact specifically with target molecules. Biological targets represent a considerable test of our knowledge of the fundamental principles of molecular recognition. Effective modulation of biological events requires the generation of molecules with both high affinity and high specificity for the desired target. Researchers in my group utilize modern methods of organic synthesis and catalysis, combinatorial synthesis and high-throughput analysis, solid-phase and expression-based peptide and protein synthesis, advanced NMR and computational analysis, molecular biology, and biological assays.

PROTEIN PHOSPHORYLATION

The complexity of humans is dependent on post-translational modifications of proteins. The most common post-translational modification is the phosphorylation of serine, threonine and tyrosine residues by protein kinases. Protein kinases are tightly regulated, and changes in kinase activity are associated with most human diseases, including cancer, heart disease, and Alzheimer's disease. We are developing approaches to understand how protein phosphorylation changes the structure of proteins toward understanding the mechanisms associating changes in kinase activity with human diseases. In addition, we are developing new tools to understand the changes in kinase activity associated with human disease. We have designed new protein structures, called protein kinase-inducible domains, whose structures are dependent on their phosphorylation state. These designed proteins are under the control of specific protein kinases and are non-fluorescent when not phosphorylated, but highly fluorescent when phosphorylated, and may act as genetically encoded sensors of protein kinase activity.

PROTEIN MISFOLDING AND DISEASE

Numerous diseases, including Alzheimer's disease, Parkinson's disease and spongiform encephalopathies (i.e. mad cow disease and its human variants), are characterized by protein misfolding and precipitation which is central to the observed pathology. We are interested in the molecular mechanisms leading from the soluble, monomeric protein to the insoluble, polymeric protein forms. We are particularly interested in understanding the molecular mechanisms of Alzheimer's disease. Alzheimer's disease is characterized by two protein aggreagates in the brain: extracellular plaques and intracellular neurofibrillary tangles (NFTs). The major protein in neurofibrillary tangles is a hyperphosphorylated version of the protein tau. Tau normally stabilizes the elongated structure of neurons by binding to the microtubules. However, hyperphosphorylation of tau, phosphorylation on over 30 residues of tau, results in structural changes in tau that cause the precipitation of tau in neurofibrillary tangles. We are examining the molecular mechanisms by which hyperphosphorylation of tau leads to structural changes, protein aggregation, and neurofibrillary tangle formation.

SMALL MOLECULE PROTEOMIMETICS

Work in genomics and proteomics is revealing vast numbers of interaction loci within the cellular milieu, and thus vast numbers of potential targets for agonists and antagonists of protein-protein, protein-DNA and protein-RNA interactions. Our focus is the use of molecular design and organic synthesis to develop small molecules which mimic larger biological structures. Our work involves the development of appropriate, readily accessible organic scaffolds, in solution and on solid phase, using modern methods of organic synthesis. To evaluate our scaffolds they are subjected to high-throughput testing for biological activity. Modularity in synthesis allows the combination of multiple structural elements to allow recognition of larger protein surfaces and the synthesis of multifunctional "proteins." The post-genomic era requires novel tools to elucidate the identity, classes and modes of protein-protein interactions in disparate cell types, developmental stages, and intracellular environments, in addition to changes due to age and disease states. The ability to generate small molecule mimics of protein recognition elements permits their use as chemical probes of protein-protein interactions.

ELECTRONIC AND STEREOELECTRONIC EFFECTS IN PROTEINS AND THE DESIGN OF TUNABLE PROTEINS

One hallmark of native, functional proteins is the adoption of a stable, highly conformationally restricted ensemble of closely related structures. In peptides, small proteins, and natively disordered proteins, where the hydrophobic effect is reduced, it is difficult to overcome the entropic cost of conformational restriction. Strategies to enable conformational restriction and stabilization of peptides and proteins may be used to interrogate protein structure-function relationships and to develop novel mediators of biological activity. We are developing new approaches to control local conformation via small peptide motifs and practical and readily applied organic synthesis. We are examining two approaches to control protein conformation: controlling main chain conformation via controlling the ring pucker of proline residues, and controlling cis-trans isomerization via tuning of proline and/or aromatic ring electronics. We have demonstrated that the interactions between aromatic residues and proline residues are controlled by aromatic electronics. We are developing approaches to tunably control the structures of peptides and proteins using stereoelectronic effects to control proline conformation and the electronic effects of aromatic rings to control the interactions between aromatic rings and proline. We are applying these approaches to stabilize protein secondary structures in peptides, to stabilize protein structures, to develop novel inhibitors of protein-protein interactions, and to design tunable proteins which are able to act conditionally, producing one structure or response in one environment and producing a contrary structure or response in a different environment.

ENANTIOSELECTIVE CATALYSIS

Effective, selective catalysis requires molecular functionality sufficient for catalytic activity, (regio- and stereo-) discrimination in substrate recognition enforced by reproducible transition state geometry, rapid association of substrate and dissociation of product to ensure turnover, and a partially open geometry to allow significant substrate scope. The incorporation of catalytic functionality within a designed structure is an important goal, and provides a critical test of our knowledge of the fundamental principles of molecular folding and catalysis. Due to their inherent chirality and structure, peptides and designed proteins are ideally situated to function as highly effective catalysts, despite limited success to date. Our approach is to design novel peptides cabable of functioning as effective catalysts. A second element to catalyst discovery is the ability to rapidly screen catalyst candidates. To address the scope of combinatorial space, both in terms of catalyst structure and substrate generality, we are developing new methods for high-throughput screening for catalysis. These methods are designed to be applicable not only to the discovery of protein- and peptide-based catalysts, but also toward the discovery of metal-complex-based catalysts and organocatalysts.

Publications

Thomas, K. M.; Naduthambi, D.; Tririya, G.; Zondlo, N. J. "Proline Editing: A Divergent Strategy for the Synthesis of Conformationally Diverse Peptides," Organic Letters 2005, 7, 2397-2400. DOI: 10.1021/ol0506720

Meng, H. Y.; Thomas, K. M.; Lee, A. E.; Zondlo, N. J. "Effects of i and i+3 residue identity on cis-trans isomerism of the aromatic_i+1-prolyl_i+2 amide bond: Implications for Type VI beta-turn Formation," Biopolymers (Peptide Science) 2006, 84, 192-204. DOI: 10.1002/bip.20382

Thomas, K. M.; Naduthambi, D.; Zondlo, N. J. "Electronic Control of Amide cis-trans Isomerism via the Aromatic-Prolyl Interaction," J. Am. Chem. Soc. 2006, 128, 2216-2217. DOI: 10.1021/ja057901y

Bielska, A. A.; Zondlo, N. J. "Hyperphosphorylation of tau Induces Local Polyproline II Helix," Biochemistry 2006, 45, 5527-5537. DOI: 10.1021/bi052662c

Balakrishnan, S.; Zondlo, N. J. "Design of a Protein Kinase-Inducible Domain," J. Am. Chem. Soc. 2006, 128, 5590-5591. DOI: 10.1021/ja057692h

Zondlo, S. C.; Lee, A. E.; Zondlo, N. J. "Determinants of Specificity of MDM2 for the Activation Domains of p53 and p65: Proline27 Disrupts the MDM2-binding motif of p53," Biochemistry 2006, 45, 11945-11957. DOI: 10.1021/bi060309g

Naduthambi, D.; Zondlo, N. J. "Stereoelectronic Tuning of the Structure and Stability of the trp cage Miniprotein," J. Am. Chem. Soc. 2006, 128, 12430-12431. DOI: 10.1021/ja0648458

Balakrishnan, S.; Zhao, C.; Zondlo, N. J. "Convergent and Stereospecific Synthesis of Molecules Containing alpha-Functionalized Guanidiniums via alpha-Guanidino Acids," J. Org. Chem. 2007, 72, 9834-9837. DOI: 10.1021/jo701766c

Zondlo, S. C.; Gao, F.; Zondlo, N. J. "Design of an Encodable Tyrosine Kinase-Inducible Domain: Detection of Tyrosine Kinase Activity by Terbium Luminescence," J. Am. Chem. Soc. 2010, 132, 5619-5621. DOI: 10.1021/ja100862u

am Ende, C. W.; Meng, H. Y.; Ye, M.; Pandey, A. K.; Zondlo, N. J. "Design of Lanthanide Fingers: Compact Lanthanide-Binding Metalloproteins," ChemBioChem 2010, 11, 1738-1747. DOI: 10.1002/cbic.201000056

Zondlo, N. J. "Fold Globally, Bond Locally," Nature Chemical Biology 2010, 6, 567-568. DOI: 10.1038/nchembio.413

Balakrishnan, S.; Scheuermann, M. J.; Zondlo, N. J. "Arginine Mimetics via alpha-Guanidino Acids: Introduction of Functional Groups and Stereochemistry Adjacent to Recognition Guanidiniums in Peptides," ChemBioChem 2012, 13, 259-270. DOI: 10.1002/cbic.201100638

Forbes, C. R.; Zondlo, N. J. "Synthesis of Thiophenylalanine-containing Peptides via Cu(I)-mediated Cross-Coupling," Organic Letters 2012, 14, 464-467. DOI: 10.1021/ol202947f

Brown, A. M.; Zondlo, N. J. "A Propensity Scale for Type II Polyproline Helices (PPII): Aromatic Amino Acids in Proline-Rich Sequences Strongly Disfavor PPII Due to Proline-Aromatic Interactions," Biochemistry 2012, 51, 5041-5051. DOI: 10.1021/bi3002924

Zondlo, N. J. "Aromatic-Proline Interactions: Electronically Tunable CH/pi Interactions," Acc. Chem. Res. 2013, 46, 1039-1049. DOI: 10.1021/ar300087y

Pandey, A. K.; Naduthambi, D.; Thomas, K. M.; Zondlo, N. J. "Proline Editing: A General and Practical Approach to the Synthesis of Functionally and Structurally Diverse Peptides. Analysis of Steric versus Stereoelectronic Effects of 4-Substituted Prolines on Conformation within Peptides," J. Am. Chem. Soc. 2013, 135, 4333-4363. DOI: 10.1021/ja3109664

Group Members

Neal Zondlo, Principal Investigator.
Christina Forbes, Graduate Student. B.S. Delaware Valley College
Michael Elbaum, Graduate Student. B.S. Rider University
Aaron Lee, Graduate Student. B.S. Shepherd University
Kara Martin, Undergraduate Researcher, University of Delaware
Anil Pandey, Graduate Student. B.S., M.S., M.Phil., University of Delhi
Monica Pirigyi, Undergraduate Researcher, University of Delaware
Anna Scott, Graduate Student. B.S. Birmingham Southern
Cay Tressler, Graduate Student. B.S. Indiana University of Pennsylvania
Drew Urmey, Graduate Student. B.S. UMBC

Group Alumni

Shalini Balakrishnan, Ph.D. 2007 (postdoctoral fellow, Derek Tan lab, Sloan Kettering)
Santosh Bhor, postdoctoral fellow 2006-2009 (Senior Scientist, ChemBioTek)
Agata Bielska, B.S. 2006 (M.D.-Ph.D. student, Washington University)
Michael Brister, B.S. 2012 (scientist, GlaxoSmithKline)
Alaina Brown, B.S. 2004 (M.D., University of Virginia, 2008; fellowship, Duke University)
Chris am Ende, B.S. 2005 (scientist, Pfizer)
Kyle Davis, B. S. 2010 (Ph.D. student, Department of Environmental Sciences, University of Virginia)
Feng Gao, Ph.D. 2010 (senior scientist, Asymchem)
Hai Yun Meng, M.S. 2006 (GenOn Energy)
Devan Naduthambi, postdoctoral fellow 2004-2008 (Senior Resesearch Scientist, Gilead Sciences)
Rebecca Salomon, B.S. 2005 (Ph.D., University of Virginia, 2010) (Senior Scientist, Department of Defense)
Michael Scheuermann, M. S. 2011 (Cytec Engineered Materials)
Krista Thomas, M.S. 2005 (Assistant Professor, Johnson County Community College)
Gasirat Tririya, postdoctoral fellow 2003-2005 (senior scientist, ASDI)
Mao Ye, postdoctoral fellow 2003-2004 (Assistant Director, Bioscience Synthetic Chemistry Core Facility, California NanoSystems Institute, UCLA)
Chen Zhao, M.S. 2005 (scientist, Wilmington Pharmatech)
Susan Carr Zondlo, senior research fellow 2003-2006 (Group Leader and Head of Efficacy and Safety Biomarkers, Department of Translational Medicine, QPS)

Lab Funding

NIH NIGMS (2010-2015)
National Science Foundation CAREER (2006-2011)
NIH COBRE
Alzheimer's Association
American Heart Association
National Science Foundation and the Intelligence Community
Undergraduate research funding: HHMI, Beckman Institute

Neal Zondlo Background

B. A. Rice University, summa cum laude, 1992. Biochemistry and Russian. (Undergraduate Research Advisors: Michael Stern (Rice), Richard L. Schowen (University of Kansas))
NSF Predoctoral fellow, Yale University, 1992-1995.
Ph. D. Yale University, 1999. (Graduate Advisor: Alanna Schepartz)
NIH postdoctoral fellow, Harvard University, 1999-2001. (Postdoctoral Advisor: Eric N. Jacobsen)

Contact Neal Zondlo

Mail:: Neal J. Zondlo
Associate Professor
234 Brown Laboratory
Department of Chemistry and Biochemistry
University of Delaware
Newark, DE 19716

Phone: 302-831-0197 (please do not leave voicemail: instead contact by email)
Fax: 302-831-6335
Email: zondlo@udel.edu (preferred contact)