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Current YearTrainees 


Alcantara, JuanJuan Alcantara

Skidmore College, Chemistry B.A., Biochemistry Concentration, Summa Cum Laude

Program/Dates Supported by NIGMS: Chemistry/ August 2022-present

Title:  Rapid rescoring and refinement of ligand-receptor complexes using mixed MD/MC with a pose reservoir

Modern drug discovery approaches commonly utilize computational methods to find or generate molecules that show favorable binding to a specified macromolecular target. Millions of molecules can be rapidly tested via a virtual screen to filter out bad binders early before purchasing or synthesizing the molecules for experimental assays. Virtual screening involves the generation of poses for a library of ligands, and ranking using simple energy functions with limited flexibility and generally, no water solvation. Top scored poses are used to rank and prioritize ligands with respect to their theoretical interaction energies with the target. The simplified electrostatics approximations and lack of solvation limit the accuracy of the virtual screening pose energy rankings, increasing incidents of choosing the incorrect pose as the most favorable one. Here we adapt an accelerated molecular dynamics (MD) method, developed for peptide folding, to enhance and refine the virtual screening pose energy ranking process. The method re-ranks the poses using the full molecular mechanics energy function and allows for receptor flexibility as well as solvation, increasing the accuracy of the predicted pose rankings relative to the simplified virtual screening protocols. ligand poses from the virtual screen are subjected to short MD equilibration and are used to populate a structure reservoir which then can be used alongside another MD simulation of the poses to allow for rapid exchanges between the conformations via Monte Carlo (MC) jumps. This allows us to circumvent the sampling time constraint of normal MD which would be too slow in generating the same poses that were already predicted by the virtual screen. Relative populations of poses can be obtained with regards to their binding interaction stability. This method provides a more accurate way to rank ligand poses to either corroborate or refine the original virtual screening rankings.

Recently we have shown that this new MD approach with implicit solvation can predict the most favorable pose amongst the ones generated in a DOCK virtual screen for systems where DOCK also chose the same pose as the favorable one. The approach was also able to select the correct pose in instances where DOCK was not able to predict it as being the most favorable. Since MD is more accurate in its sampling dynamics, the pose rankings and favorability observed during the MD simulations can be used as a guide to determine whether the initial DOCK screening was accurate or if the rankings could benefit from MD refinement. Although this approach showed success with implicit solvent, ongoing work will focus on using explicit solvation to account for systems that may have critical water molecules mediating ligand binding, as well as developing an additional approach to account for residue protonation states in cases where shifted pKa’s in the active site are ambiguous. Further in the future this MD method will be adapted for use in estimating relative binding affinities for different types of ligands  rather than just different conformations of the same one. This will allow for the comparison of very distinct ligands which is not feasible with current free energy methods that rely on ligands having similar scaffolds.

RaquibKindra Becker

B.A. in English Literature, Master of Library and Information Science, University of South Carolina

Program/Dates Supported by NIGMS: Chemistry/ August 2022-present

Title: Synthesis of Fluorophores for APEX2 Proximity Labeling in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the second leading infectious killer after COVID-19. The rise of multi-drug- and extensively drug- resistant cases of TB reveal a pressing need for the development of new drugs against Mtb. Although an attractive drug target is the unique diderm envelope that harbors essential processes like uptake and export of metabolites, the mycobacterial cell wall proteome is not well-elucidated. In determining the proteome of the cell wall, we can identify these essential processes and, within these, potential drug targets. Our lab has successfully used proximity labeling with APEX2, an engineered peroxidase, to label proteins in a compartment-specific manner. To expand our understanding of the mycobacterial cell envelope, we have genetically encoded APEX2 to an outer membrane protein, MspA. Biotin-phenol, a commonly used APEX2 substrate, is cell permeable, labeling proteins in both the periplasm and cell wall. Considering this, we hope to synthesize a substrate that is unable to enter the cell. Here, we use the coupling reagent N-N’diisopropylcarbodiimide (DIC) to activate a carboxylic acid and react with a free amine to form an amide bond. 5-aminofluorescein (FAM) was chosen as the basis for the cell impermeable substrate because of its hydrophilicity and anionic charge at neutral pH. As a control, the starting material 7-hydroxycoumarin-3-carboxylic acid was chosen for its ability to cross the mycobacterial membrane. These products, FAM-phenol and 7-hydroxycourmarin-phenol, will hopefully help us cross the final frontier to understanding uptake and export at the mycobacterial cell surface.

Cao, MinhuaMinhua Cao

BA Chemistry, Hunter College of City University of New York - 2019

Program/Dates Supported by NIGMS: Chemistry/ August 2021-present

Title:  Metallophores as tools for antibiotic drug development and the study of bacterial metal homeostasis

The Microbial infection is closely tied to nutrient acquisition. Bacteria rely on iron acquisition from the host for survival, the host iron is sequestered as Fe3+ by bacterially produced metallophores termed siderophores. While biding Fe3+ efficiently, siderophores also present high affinity toward other metal ions such as Ga3+, Sc3+, and In3+ which share similar size and coordination chemistry with high-spin Fe3+. Previous studies have shown these Fe3+ mimics display growth inhibitory activity.  The over-arching goal of my project is to investigate how the metallophore-mediated transport of Ga3+, Sc3+, and In3+ takes advantage of the iron siderophore acquisition mechanism and identify which cytoplasmic targets are affected that result in the observed growth-inhibitory activity. To address these questions, we aim to develop metallophore probes designed to incorporate a 67Ga or 124I label for metabolic tracking and photoaffinity probes incorporating a fluorescent diaziridine photoaffinity tag, for the isolation and identification of proteins involved in active trans-membrane transport. These metallophore probes have the potential to be useful tools to uncover siderophore conjugate mechanism of action and further improve their efficacy.

Corbo, ChristopherChristopher Corbo

B.E. in Chemical & Molecular Engineering, Stony Brook University

Program/Dates Supported by NIGMS: Biochemistry and Structural Biology/ August 2021-present

Title:  Dynamic scoring for de novo design of molecules

Computer aided drug design is an integral part of modern drug discovery, particularly for hit identification. A hit is typically defined as a molecule which has a micromolar affinity for a protein target and is a starting point for optimization. This stage of drug development is particularly amenable to the use of computational techniques as they can search large areas of chemical space in a quick and efficient manner. My research aims to further improve this process via the development of new routines and algorithms in DOCK6. 

One such method for hit identification is the fragment by fragment construction of molecules within the constraints of a binding site, called de novo design. Currently DOCK6 can bias the construction of molecules towards those which are more similar to a given reference molecule, such as an experimentally validated inhibitor. This is achieved through the use of similarity-based scoring functions which assess the similarity of growing molecules to the reference molecule. Those which are most similar are advanced to subsequent stages of growth. However this inadvertently creates a bias for molecules which are bulkier at early stages of growth, and leads to ill-informed decisions. I believe that by reconstructing the reference molecule in parallel to the growth of new molecules, a higher degree of similarity can be achieved. This dynamic scoring will further focus the search for new hits in areas of chemical space which are likely to be successful, while still identifying novel chemical structures.

GilbertiYongLe He

BS in Chemistry, Stony Brook University, 2019

Program/Dates Supported by NIGMS: Chemistry/ January 2022-present

Title:  Mechanistic studies of BLUF and LOV photoreceptors and photoswitchable fluorescent protein

Photoreceptors are light-sensitive proteins that contain a chromophore responsible for sensing and responding to light in a variety of organisms. They have unique applications in the field of optogenetics where light can be used to modulate biological functions. My research involves the characterization of two groups of photoproteins: the blue-light using FAD (BLUF) and light oxygen voltage (LOV) domain photoreceptors where excitation results in structural changes that ultimately lead to biological processes such as photosynthesis, visual transduction, and circadian rhythms. For the BLUF and LOV proteins, our aim is to elucidate the signaling transduction mechanism from the chromophore binding domain to the effector domain using time-resolved infrared spectroscopy combined with chemical and structural biology techniques. Currently, we are investigating multiple BLUF (AppA, PixD, and BlsA) and LOV (AsLOV2, YtvA, and El222) proteins. Also, we are correlating the structural activity relationship of the photoactivated domain with the functionally relevant effector domains, such as PixD-PixE complex (controls phototaxis), AsLOV2-PAC1 (optogenetic construct), YtvA-FixL1 (histidine-phosphotransferase and Kinase), and El222-DNA complex (transcriptional factor).

In addition, we also study the photoswitchable fluorescent protein that can be reversibly switched between bright and dark states.  The main goal is to characterize the photoswitching mechanism in Dronpa2 using vibrational spectroscopy (IR and Raman), isotope labeling, and unnatural amino acid incorporation. Previously, we successfully used IR and Raman spectroscopy to explain the photoswitching isomerization of the Dronpa chromophore, and we want to extend our study to its homolog Dronpa2. Ultimately, this knowledge can drive the development of more optogenetic tools and the application of photoswitchable proteins in super-resolution microscopy.

LuperchioAdeline Luperchio

B.S. in Microbiology, University of Vermont

Program/Dates Supported by NIGMS: Chemistry/ August 2022-present

Title: Critical HIV-1 Vif interactions: Molecular approaches to novel HIV therapies

Like all viruses, HIV-1 hijacks cellular machinery to facilitate replication and evade host antiviral defense mechanisms. HIV-1 deploys several accessory proteins that manipulate the cellular environment to enhance virus replication. The accessory protein Vif is responsible for counteracting host antiviral APOBEC3 enzymes to promote virus replication. In the absence of Vif, APOBEC3s package into nascent HIV-1 particles and hypermutate the viral genome to kill the virus. Vif counteracts APOBEC3 restriction by targeting them for proteasomal degradation prior to virus encapsidation. Quantitative proteomics studies of HIV-1 infected T cells recently revealed that Vif also induces remodeling of the host phosphoproteome by inactivating protein phosphatase 2A (PP2A) complexes. PP2A is responsible for the vast majority of cellular serine/threonine dephosphorylation events in most cell types. How phosphoproteome remodeling enhances HIV-1 replication has yet to be resolved.

Another recently ascribed Vif interaction is with the cellular kinase AKT. Vif stimulates hyperactivation of AKT to trigger a feedback loop wherein AKT phosphorylates Vif to enhance its stability. Interestingly, inhibition of AKT leads to a complete loss of Vif protein accumulation; however, the molecular mechanism driving this process has yet to be elucidated. My preliminary data indicates that Vif-induced inactivation of PP2A triggers hyperactivation of AKT. Thus, I’m interested in if the Vif-PP2A-AKT network can be leveraged as a therapeutic target to deplete Vif protein levels and restore antiviral activity of APOBEC3 restriction factors. The Aims of my research are to 1) use biochemical, genetic, and pharmacologic approaches to investigate the Vif-PP2A-Akt nexus and 2) identify small molecule inhibitors that disrupt the Vif-PP2A interaction. These mechanistic insights may inform the development of novel strategies that restore restriction activity of the APOBEC3 enzymes, potentially taking the next step towards curative therapeutics.

OuthwaiteIan Outhwaite

B.A. Williams College, 2017

Program/Dates Supported by NIGMS: Chemistry/ August 2022-present

Title: Maximizing Selective Inhibition of Clinically Observed MET Mutants

Mesenchymal epithelial transition factor (c-MET/MET), a receptor tyrosine kinase, is an oncogenic driver in numerous tumor types, notably non-small cell lung cancer (NSCLC) and melanomas. On-target mutations drive resistance against small-molecule MET inhibitors. I aim to comprehensively profile the selectivity of clinically approved MET inhibitors against MET mutants, and determine combinations of these inhibitors that maximize on-target activity and reduce off-target effects.

This work will provide a rationale for targeted clinically approved tyrosine kinase inhibitor combinatorial therapies against MET mutants. Indicated combinations of clinically approved inhibitors will 1) maximize on-target activity, 2) reduce off-target effects, and 3) circumvent the development of tyrosine kinase inhibitor resistance. These inhibitor combinations may provide a direct translational benefit for patients with MET-driven cancers, or those in which MET signaling represents an escape mechanism following therapy against other targets (ex: EGFR, ALK).

RaquibRideeta Raquib

B.S. in Interdisciplinary Biology, Stony Brook University

Program/Dates Supported by NIGMS: Chemistry/ August 2022-present

Title:  Evaluating the Structure and Activity of Diacylglycerol-O-Acyltransferase 2 (DGAT2) in Various Lipid Membrane Environments

Triglycerides (TGs) are the main chemical form of long-term energy storage and are stored intracellularly in lipid droplets (LDs). TG accumulation is linked to various diseases including cancer, diabetes, cardiomyopathy, and obesity.  LDs are generated in the endoplasmic reticulum (ER), where most of the enzymes involved in TG synthesis are located. This includes Diacylglycerol-O-Acyltransferase 2 (DGAT2), a monotopic membrane protein that catalyzes the last and only committed step of TG biosynthesis. Specifically, DGAT2 catalyzes the formation of an ester linkage between a fatty acyl-coA and 1,2-diacylglycerol (DAG), not only on the cytoplasmic face of the ER, but also on the surface of LDs, when fatty acids are in excess. Alternatively, DGAT2 can utilize pro-apoptotic ceramide as a substrate, instead of DAG, to generate 1-O-acylceramide, which has been implicated in causing cancer cells to become resistant to chemotherapy.  Given DGAT2’s prominent roles, it serves as a strong candidate for therapeutic targeting. Although we have a general idea about the function and localization of DGAT2, little is known about its structure, the residues that facilitate selective substrate binding (e.g. DAG vs ceramide), and if catalytic activity is altered by diverse membrane environments (e.g. ER lipid bilayers vs. LD lipid monolayers).  We plan to address these questions biochemically, using purified human DGAT2 and/or a thermophilic DGAT2 homolog from C. thermophilum (Ct DGAT2).  We were able to detergent solubilize and purify recombinant human DGAT2 and Ct DGAT2. We developed enzymatic assays using both TLC and liquid chromatography-mass spectrometry (LC/MS) and confirmed purified Ct DGAT2 is catalytically active.

Further, we reconstituted the enzyme into various membrane environments, such as liposomes and artificial lipid droplets to mimic ER and LD membranes. Eventually, we plan to determine the structures of active DGAT2 alone and bound to its substrates and/or inhibitors using X-ray crystallography. Our hope is that in the future, this research will pave the way for the development and classification of potent DGAT2 inhibitors, with optimized mode of delivery to LDs and ER membranes, that can improve treatment efficacy for cancer, and other diseases associated with TG accumulation.

WithornJason M. Withorn

BS Biochemistry and Chemical Biology from Wayne State University in Biology, Pepperdine University

Program/Dates Supported by NIGMS: Chemistry/ July 2021-present

Title:  Functional characterization of the NosP associated histidine kinase, NahK, and its role in biofilm formation in Pseudomonas aeruginosa

Biofilms are multicellular communities formed when bacteria attach to a surface and secrete a thick, mucoid protective barrier known as the exopolysaccharide matrix (EPS). The EPS is composed of polysaccharides, extracellular DNA, and proteins. The EPS encompasses the cell promoting a nutrient rich environment that prevents antibiotics from reaching the cell.

It has been shown that the diatomic gas, nitric oxide (NO), facilitates the dispersal of biofilm-forming bacteria, reverting to a planktonic state. In 2017, our group discovered a novel heme-binding protein named NosP, nitric oxide sensing protein which functions to inhibit the NosP associated histidine kinase, NahK, which is located on the same operon. Our group has shown that when these two proteins are deleted, the bacteria are unable to form complex biofilm structures and they lose the ability to respond to toxic levels of NO. My project focuses on the pathogen Pseudomonas aeruginosa, which has been identified as a priority one pathogen needed a new treatment according to the World Health Organization. My project focuses on elucidating the function of NahK in vivo, and determining the role of the three uncharacterized PAS sensory domains located on the kinase.  Understanding how NahK’s function in regards to signaling changes could allow for a more in depth understanding of NO-mediated biofilm dispersal, and allow for a more efficient treatment of biofilms to be developed.


Active Trainees 


Francis Boadi CBTP 2020John Bickel

BS in Chemistry, Truman State University

Program/Dates Supported by NIGMS: Chemistry/ 2020-2021

Title:  Strategies for biasing de novo design in DOCK6

The goal of my proposed research is to further develop and improve the from-scratch construction algorithm (de novo design) as currently implemented in DOCK6 for the purposes of constructing potential compounds designed for a specific target. As libraries of compounds on public databases such as ZINC15 continue to grow in size at an astounding rate (currently ~750M), performing a full virtual screen of these libraries against potential drug targets is becoming increasingly infeasible given the current docking architecture. By constructing these compounds directly to the site of interest, there is a higher probability of the resulting compounds to have higher specificity and tighter binding interactions.

The ultimate goal in improving and optimizing the DOCK6 de novo algorithm is to be able to effectively bias construction of new molecules such that populations of newly constructed torsion types (allowable bond types) more closely match the distribution of torsions of an input library derived from drug-like compounds. This goal is being addressed by implementation of a fitness proportionate (roulette) method of selection, as well as implementation of new ways of handling DOCK6’s database of fragments and their associated bonding pairs.

Francis Boadi CBTP 2020Francis Boadi 

BA in Chemistry, Rutgers University

Program/Dates Supported by NIGMS: Chemistry/ 2019-2021

Title:  Developing pH-sensitive copolymers and glycopolymers with sequence-defined backbone

A significant number of pH sensitive polymers are biodegradable. For this matter, they have the potential to play relevant roles in life. Biodegradable polymers/plastics have been championed in the last four decades owing to a myriad of opportunities they present including environmentally friendly and biocompatibility. Generally, there are two classes of biodegradable polymers which are natural and synthetic. Synthetic polymers offer more advantages than natural polymers because synthetic tool offers handles to modify and functionalize polymers to suit certain applications. To an extent, with synthetic tools, we can bridge the gap between natural and synthetic polymers. Notable synthetic biodegradable polymers are poly-L-lactic acid (PLLA), polyglycolic acid (PGA)/polylactic acid (PLA), polycaprolactone (PCL). These polymers are mostly synthesized by condensation techniques which makes it somewhat impractical to prepare polymers with incredibly high mechanical strength. For this reason, we sought to develop methodology which would enable us to prepare very long high molecular weight polymers which are readily degradable. Our group has developed a type of polymerization called alternating ring opening metathesis polymerization (AROMP). Together with my colleague, Jingling Zhang, we have successfully prepared high molecular weight polymers using AROMP. What is interesting is that these polymers have ester and acetal functionalities in their backbone which are readily degradable under basic and acid conditions respectively. This would possibly have applications in drug delivery and lithographic patterning.

Synthetic tools provide handles to have access to natural polymers. Multivalent sugars have shown to have better efficacy compared to monovalent sugars. Using polymerization method such as ring opening metathesis polymerization (ROMP) and norbornene as the backbone scaffold. Our group has developed several sugar polymers. These glycopolymers, mannose, fucose, GlcNAc, have shown to induce acrosomal exocytosis of male sperm. Galactose and fucose polymers have also shown to bind to cholera toxins. The mechanism of action in these cell binding processes are not well understood. The glycopolymers used in these studies are based on polynorbornene scaffold which tend to lack sequence-definition. Nature’s heavy reliance on sequence have caused us to reason that having sequence-control in our glycopolymers’ backbone would enhance their efficacies. Therefore, my goal is to use AROMP to prepared and sequence sequence-defined copolymers of sugars.


Danielle pic

Danielle Cervasio

BS, summa cum laude,  SUNY Cortland, 2017

Program/Dates Supported by NIGMS: Chemistry/ 2018-2021

Title:  Translational applications of small-molecule, astrocyte-targeted probes

Astrocytes are the most abundant non-neuronal cell type in the brain, providing support, nutrient buffering, and instructions to neighboring cells, particularly neurons, in order to maintain normal physiological function and homeostasis. Importantly, astrocytes play a large role in the brain by responding to insult, communicating with neurons via gliotransmitters, and forming protective barriers around endothelial cell layers. Because astrocytes are present abundantly in all cortical areas of the brain, performing essential metabolic, structural, and homeostatic roles, it is not surprising that they are implicated in a slew of disease and disorders, including, but not limited to, Alzheimer’s, Parkinson’s, glioblastoma, stroke, seizure, infection, and depression. Thus, it is becoming increasingly important to consider these cells for therapeutic intervention of such disease, seeing that they are important players in maintaining normal brain function. In leveraging organic cation transporters (OCTs) on the surface of astrocytes, we have developed a system by which a permanently positive N-heterocyclic amine can be attached, via organic chemistry, to diverse small molecules like fluorophores, photoactivatable markers, or calcium indicators and delivered specifically to astrocytes over neurons and other glia (Fig. 1a and b). These data have inspired us to think about more translational applications, including the potential to deliver drugs or transcription activators to astrocytes for therapeutic intervention. Gene-targeted therapies are currently in the clinic, but there exists a lack of regulated systems. We currently have some control over where, but no control over when therapeutic genes are expressed. I plan to synthesize and assay a doxycycline modified with a permanently positive N-heterocycle to exploit the powerful tetracycline-inducible gene expression system (Tet-On/Off) in order to control gene expression in astrocytes, exclusively. In adding this modification, I hypothesize that we will be able to target astrocytes for therapeutic intervention, decrease concentrations of drug needed by increasing blood brain barrier (BBB) penetration, and reduce off target effects of current constitutively active therapies as seen in Glial cell-derived neurotrophic factor (GDNF) or Neurturin (NTN) gene therapy for Parksinson’s disease.  
Danielle graphic


Francis Boadi CBTP 2020Jiayuan Fu

BS, Beijing Normal University, 2018

Program/Dates Supported by NIGMS: Chemistry/ 2019-2021

Title:  Characterization of a Novel Nitric Oxide/Heme Sensing Protein and its Role in
Regulating Biofilm Formation in Burkholderia Thailandensis

Bacteria use two-component system to sense and respond to environmental cues. Two component systems usually are composed of sensory histidine kinase and response regulator, the effecter domain of the latter is tightly regulated by its phosphorylation state. Two-component systems modulate bacterial physiological processes including motility, biofilm formation and virulence factor secretion. Particularly, a lot of these processes are indirectly controlled by two-component system via the production or degradation of secondary messengers, one of the examples is cyclic-di-GMP, high level of which contribute to robust biofilm formation in most bacteria species. As biofilms are surface attached microorganisms that are shielded within extracellular polymeric substances, they cause a lot of antibiotic resistance. People are getting interested in using small molecules to trigger the dispersal of biofilms, one of the most promising one is nitric oxide.

We identified a two-component system and its co-cistronic sensor protein NosP from Burkholderia thailandensis, the close surrogate of highly infectious Burkholderia pseudomallei which cause serious tropical disease melioidosis. We proved successful kinase autophosphorylation and phosphoryl transfer from the kinase to the receiver domain of response regulator. By site-directed mutagenesis, we were also able to identify the key residues that contribute to the phosphorelay, which are a histidine from the kinase and an aspartate from the response regulator. The cognate sensor protein of this two-component system, which termed as NosP, is a heme-based sensor which possibly conduct signaling transduction to the kinase via protein-protein interaction. NosP uses label heme as signaling molecule, as heme-bound NosP inhibit kinase autophosphorylation while apo-NosP does not. NosP displayed very fast heme dissociation rate, much faster than that of obligated heme proteins such as sGC and myoglobin. NosP also displayed very fast nitric oxide dissociation rate, comparable to that of well characterized NO sensor that could detect nano to picomolar nitric oxide.

In the future, we would like to know whether NO-ligated NosP will modulate kinase activity. We will also test the activity of the effector domain of the response regulator, as sequence analysis indicate a conserved phosphodiesterase motif within the effector domain that could possibly degrade c-di-GMP. We would also like to know how phosphorylation regulate the effector domain activity. Finally, we would like to know how NosP-based NO/Heme signaling regulate biofilms.

GilbertiAlexa Gilberti

BS in Chemistry, Stony Brook University, magna cum laude

Program/Dates Supported by NIGMS: Chemistry/ July 2020-2022

Title:  Targeted protein Degradation of SMG-1

Serine/Theonine protein Kinase one (SMG-1) is involved in nonsense mediated mRNA decay (NMD) which is one of the DNA Damage Response (DRR) pathways in mammalian cells.  The DDR serves to detect, fix, or ameliorate errors that may arise during DNA replication, and if left unchecked can lead to cell cycle arrest, regularion of DNA replication, and the failure to repair of DNA damage.  DDR plays an important role in protecting cancer cells from chemotherapeutics, and the underlying hypothesis of this project is that inhibition of SMG-1 will senstive cancer cells to cancer therapies as well as the immune response.  However, efforts to evaluate this hypothesis using genetic knockouts in breast cancer cells have been hindered by the essentiality of SMG-1.

Proteolysis targeting chimeras (PROTACs) utilize the cells natural ubiquitin proteasome system for protein degradation and maintaining homeostasis in the eukaryotic cells, in order to force the initiation of a degradation cascade on a target. In order to determine if SMG-1 is a suitable target for PROTAC development, we will utilize the Achilles TAG (aTAG) tool that was developed by C4 Therapeutics to knockdown the SMG-1 protein. A fusion protein of the aTAG with SMG-1 will be created using CRISPR/Cas9, and PROTACs directed at the aTAG will be used to degrade the aTAG/SMG-1 fusion protein. Targeted protein degradation with PROTACs will be used to chemically knockdown SMG-1 and evaluate SMG-1 as a potential therapeutic target.

GunawhardhanaNipuni Gunawardhana

BS in Chemistry, University of Colombo, Sri Lanka

Program/Dates Supported by NIGMS: Chemistry/ 2020-2021

Title:  Astrocyte Specific Delivery of Methyl-Pyridinium Tagged Small-Molecule Cargo

Neurons were the big players in neuroscience research until recent efforts identified that astrocytes too are active players in brain function. Astrocytes are the most abundant type of non-neuronal cells in the brain. In addition to maintaining blood-brain barrier integrity and providing nutrients to the surrounding cells, astrocytes form a specialized structure with pre- and post-synaptic neurons known as the tripartite synapse where they take part in the uptake and release of neurotransmitters. Astrocytes have been implicated in many neurological diseases  like Parkinson’s disease (PD), Alzheimer’s disease (AD), Amyotrophic lateral sclerosis (ALS), glioblastoma and depression. Accordingly, to understand how the brain circuitry functions it is essential to study astrocytes.

However, only a limited number of strategies are available for astrocyte visualization and manipulation. These existing methods lack specificity and versatility. A new class of methyl-pyridinium tagged fluorescent markers has been developed in our lab that shows specific targeting and visualization of astrocytes. The positive charge of the methyl-pyridinium targeting moiety of this probe allows active transport of diverse cargo such as Ca2+ sensors, small molecule drugs and transcriptional activators to astrocytes through the astrocyte resident Organic Cation Transporter (OCT).

I am currently synthesizing a methyl-pyridinium tagged cyanodoxycycline to activate transcription of specific genes in astrocytes using the tetracycline-inducible gene expression (Tet-On) system. My work is also focused on the drug tamoxifen to create a traceless astrocyte delivery strategy. These molecules will help us to evaluate the ability of the targeting moiety to deliver drugs specifically to astrocytes. This strategy will be beneficial for exploring the therapeutic aspects of astrocytes in various neurological diseases and will improve our understanding of the functions of astrocytes in the brain.

Kirsten Martin CBTP 2020Kirsten Martin

BS in Chemistry

Program/Dates Supported by NIGMS: Chemistry / 2019-2021

Title:   In Situ Excitation of Luminescent Lanthanide Complexes: Towards Enabling In Vivo Bioimaging

Optical imaging probes are indispensable tools for the visualization of biomarkers of disease without perturbing the biological system. Ideal optical imaging probes provide low limits of detection, minimal photobleaching and emit in the first or second biological window (550-800 nm and 1000-1350 nm). Luminescent lanthanides exhibit many of these aforementioned properties, however, as f-f transitions are Laporte-forbidden, organic chromophores absorbing in the 200-300 nm range, known as antennae, are necessary for efficient excitation of the metal ion. These excitation wavelengths are not compatible with biological applications due to the strong absorbance of proteins and hemoglobin at wavelengths below 550 nm. To circumvent this, we proposed that lanthanide-based complexes could be excited in situ using Cherenkov radiation. Cherenkov radiation is generated by charged particles emitted during the decay of radioisotopes in dielectric media in the form of the emission of short wavelength light with a maximum below 400 nm. In situ excitation of lanthanide complexes with Cherenkov radiation energy transfer (CRET) eliminates the need for external high energy, short wavelength excitation.

Following our initial proof of concept, we have demonstrated that CRET is suitable to excite discrete Tb and Eu complexes with a detection limit of 5 nmol and 10 nmol, respectively. We have demonstrated efforts towards the application of these complexes for multiplexed imaging and the targeted in vitro and in vivo imaging of prostate cancer by targeting the prostate-specific membrane antigen (PSMA). The targeted and nontargeted europium and terbium-based probes produce moderate quantum yields (10-47%) and are efficiently excited with Cherenkov radiation with radioisotopes 18F and 89Zr.  The lanthanide-based emission was monitored and quantified using a small animal fluorescence imager. With only 10 μCi of 18F, quantities as low as 10 nmol of Eu and as low as 5 nmol Tb complex can be detected. These LOD’s compare favorably with optical chromophores requiring external excitation. Stability assessments and cell binding assays of the complexes are ongoing.

Luz photoLuz Mendez 

BA with honors, Wesleyan University, 2017

Program/Dates Supported by NIGMS: Chemistry/ 2018-2021

Title:  Identifying Inducers of the Acrosome Reaction in Human Sperm with Synthetic Glycopolymers

 The acrosome reaction (AR) in spermatozoa is an essential process in mammalian fertilization. Although the mechanism behind the activation of AR is not well-understood, it is known that the glycoproteins surrounding the egg cell’s zona pellucida (ZP) can mediate the activation of AR through a series of carbohydrate binding events with the receptors on the sperm plasma membrane. Previous research in the Sampson lab has demonstrated that AR in mouse sperm can be induced successfully in vitro with the aid of glycopolymers. These glycopolymers, synthesized by ring-opening metathesis polymerization (ROMP), possess norbornene backbones and resemble terminal residues of the sugar moieties present on the ZP. These glycopolymers are hypothesized to be potential inducers of AR in human sperm. To determine the efficacy of AR induction by glycopolymers, a flow cytometry assay is currently under development, which will allow for efficient sorting and quantitative analysis of dead, live, and acrosome-reacted cells. With the aid of this assay, promising AR inducers can be identified and will allow for the distinction of sperm that are able to participate in fertilization and those that are not. The development of this flow cytometry assay will ultimately provide the clinical community with a new method of assessing male infertility that can predict AR activation, thus improving current techniques used for diagnosis and treatment.

Luz graphic

Francis Boadi CBTP 2020Steven Pak

PharmD , St John’s University, 2016

Program/Dates Supported by NIGMS: Molecular and Cellular Pharmacology/ 2020-2022

Title:  Virtual screening of small molecule inhibitors for mutated fibroblast growth factor receptor 2 in intrahepatic cholangiocarcinoma

My goal of my proposed research is to discover small molecule inhibitor for mutated fibroblast growth factors 2 in intrahepatic cholangiocarcinoma patients (ICC). ICC is a deadly liver cancer that includes very few treatment options. A large group of patients that presents all types of liver malignancies present ICC. Without adequate treatment, life expectancy after diagnosis is very short. Currently, there are no specific inhibitors for the mutational active FGFR2. Therefore, the goal of this project is to design small molecular candidates through virtual screening to bind to the binding site of the mutated FGF2.

By utilizing crystallographic structures of hyperactive FGFR2, structural models were prepared for docking simulations. Because mutated FGFR2 does not exist, additional models will need to be created for simulation. Then, large-scale virtual screening of commercially available compound libraries will be used to identify potential drug-like ligands. After virtual screening, results were ranked ordered via relevant scoring functions. Then, subsets of the most promising ligands will be purchased and tested for activity.

ParkinLia Parkin

B.A., cum lade, Cell & Molecular Biology, Barnard College, Columbia University, 2018

Program/Dates Supported by NIGMS: Molecular Genetics and Microbiology / 2020-2021

Title:Towards understanding the lipid transport pathway LprG-Rv1410c in mycobacteria, and its contribution to outer membrane biogenesis, membrane permeability, and antibiotic susceptibility

Mycobacteria, including the human pathogen Mycobacterium tuberculosis (Mtb) that causes tuberculosis (TB), have a complex and impervious double membrane that distinguishes them from Gram negative and Gram positive bacteria. Unfortunately, Mtb infects one fourth of the global population. More disturbingly, new cases of Mtb are increasingly resistant to frontline therapies. By elucidating mycobacterial membrane biogenesis pathways, we can reveal new drug targets and identify proteins that control membrane permeability.

The Jessica Seeliger lab focuses on the LprG & Rv1410c proteins, which form an operon and likely work together to transport lipids to the outer membrane of mycobacteria, more specifically referred to as the mycomembrane. Loss of the LprG-Rv1410c operon leads to attenuation in vivo and a growth defect under nutrient limitation in vitro. We recently used a computational docking screen in search of commercially available small molecule inhibitors of LprG. We discovered molecules that inhibit mycobacterial growth in an LprG-dependent manner with micromolar affinity, indicating that LprG can be specifically inhibited. Additionally, we found that a single residue in the cavity of LprG mediated interaction with one of our most potent compounds. Overall, despite having a large and generally hydrophobic pocket, LprG can be realistically inhibited and rational drug design is feasible.

Understanding LprG-Rv1410c mediated lipid transport is also of interest because these proteins are predicted to be important for intrinsic resistance to multiple TB antibiotics. It has also been shown experimentally that the loss of the LprG-Rv1410c operon leads to increased susceptibility to certain antibiotics. Therefore, targeting or inhibiting LprG-Rv1410c may promote the efficacy of antibiotics that normally cannot cross the mycomembrane efficiently.

In future studies, we will determine how LprG & Rv1410c mechanistically mediate lipid transport, in order to obtain a model of mycobacterial lipid transport to the mycomembrane. Additionally, we will investigate how LprG & Rv1410c affect membrane permeability in order to better understand drug diffusion across the mycomembrane. Ultimately, this work will better define mechanisms of mycobacterial membrane biogenesis and drug uptake. 

Francis Boadi CBTP 2020Rachel White

BS in Biology, Pepperdine University

Program/Dates Supported by NIGMS: Molecular Genetics and Microbiology/ 2020-2022

Title:  The Role of Host Protein TFII-I in Adenovirus Infection

For successful viral replication to occur, viruses must be able to subvert host cell immune mechanisms. In Adenoviruses, a family of nonenveloped DNA viruses, the Adenovirus early protein E4ORF3, a SUMO E3 ligase, has been shown to inhibit host responses that could otherwise block viral replication.  Examples of targets with known functions include several involved in detecting and repairing double-strand DNA breaks, such as the Mre11-Rad50-Nbs1 (MRN) complex and p53. If not inhibited by the virus, these proteins can negatively impact Ad replication by responding to the virus’ double-stranded DNA genome as they would to a chromosomal double-strand DNA break. E4ORF3 also targets PML nuclear bodies, which are involved both in cell responses to DNA damage and in transcriptional regulation and antiviral responses such as the interferon response.  Another major target of E4ORF3 is the transcription factor TFII-I, which suggests that it is involved in suppressing Ad infection. TFII-I is involved with multiple transcription pathways, including some activated by p53 in response to DNA damage, and can inhibit the transcription of the Ad protein L4, which is important for the transition between early and late viral transcription in Ad infection.  Some studies have also associated TFII-I with the DNA Damage Response that the MRN complex functions in. However, its exact function in Ad infection is not known, and represents an important area of research to better understand the cellular mechanisms involved in Ad infection and possible general functions of TFII-I in viral infections. 

Our lab has already created TFII-I CRISPR knockouts in normal human bronchial epithelial cells (NHBEC), and Ad strains that lack E4ORF3. I am also currently developing TFII-I CRISPR knockouts in small airway epithelial cells (SAEC). The goal of my project is to investigate cellular antiviral responses to Ad infection and Ad expression of early and late viral proteins both with and without TFII-I and E4ORF3 expression.  Such investigation has the potential to increase our understanding of TFII-I as an anti-viral effector protein and of cellular mechanisms with the potential to block DNA viruses from successfully completing infection.


 The CBTP at SBU is made possible by a generous grant from the

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