Niu Research Laboratory | University at Albany

About

The Niu research group is multidisciplinary, combining biochemistry, electrophysiology, molecular biology, molecular folding/docking, and neuroscience to study significant problems in human health. A major focus of our current study is on glutamate ion channel proteins. These channel proteins are indispensable to brain activities such as learning and memory, and malfunction of these proteins has been implicated in neurological diseases such as ALS, stroke, epilepsy, and neuropathic pain. We are working on project areas with broader impact potential, such as structure-function relationship of glutamate ion channels and drug discovery, by developing RNA aptamers and small-molecule regulatory agents (i.e., both positive and negative regulators) as potential drug candidates. RNA hydrogel becomes one of the projects stemmed from our discovery that an RNA aptamer discovered in our group is capable of self-assembling into RNA hydrogel. We are also testing highly potent and highly selective RNA aptamers we have discovered with animal models of human diseases, e.g., amyotrophic lateral sclerosis (ALS) and spinal cord induced neuropathic pain, through tissue and behavioral studies.

Research

Structure-function relationship of glutamate ion channels

The three-dimensional structure of a protein defines not only its size and shape but also its function. Understanding the relationship between protein structure and function is one of the foremost challenges in finding ways to regulate the in vivo function of a protein with precision. Projects in this area of our lab are focused on rapid kinetic measurement of the channel-opening rate on the microsecond time scale by using a laser-pulse photolysis technique with “cage glutamate.” These measurements are essential towards a better understanding of the mechanism of action for various subunits/isoforms of glutamate ion channels and developing effective means and molecular reagents to precisely control the function of various isoforms and subunits of these glutamate ion channel receptors. Currently, we are focusing on AMPA and kainate receptor subtypes and their isoforms in each subtype.

A graphic showing various images, including three graphs showing chemistry data and three chemical compounds labeled M, O and E sites.

Developing small-molecule, regulatory agents (inhibitors and potentiators) as potential drug candidates

This area focuses on developing small-molecule compounds and understanding the mechanism of action as well as the site of interaction with receptor targets. The goal is to modulate the activity of the target in vivo with high potency and selectivity. These small-molecule compounds, prepared by synthetic chemistry, are potential drug candidates for a number of neurological diseases such as amyotrophic lateral sclerosis (ALS), epilepsy and stroke. Positive modulators are potential drug candidates for cognitive deficiency such as memory deficits in Parkinson’s disease. We also characterize the structure-activity relationship for these compounds.

An infographic with two parts. The first graphic depicts the Transient Transfection of HEK-293 Cells with GluR2 and TAg Genes. The intact GluR2 are embedded in cell membrane and bonded with RNA Library. Through Elution by NBQx, the Bound RNA become Eluted RNA. Through RT-PCR, the Eluted RNA become DNA, which undergoes a cloning sequence and transcription to become the RNA Pool. The second graphic depicts a full AB9 becoming an AMPA receptor and pieces AB9s becoming an AMPA receptor and KA receptor, and two

RNA: Aptamers as potential drug candidates

One of the core components in our research is the discovery of RNA molecules as water-soluble, potent and selective antagonists or positive modulators (potentiators) of glutamate ion channels. We use SELEX technique to isolate these useful aptamers from a large RNA library (about 1,014 sequences). We also make chemically modified RNA aptamers by replacing 2’-OH group in ribose so these RNA aptamers are long lasting and are therefore amenable for in vivo use as drug candidates for CNS diseases.

An infographic with three examples of DNA sequencing, six images of complex chemical compounds, and five graphics showing an RNA ladder, a mathematical graph, two chemistry equations, and illustrations of unblocked and blocked glutamate binding sites.

RNA: Folding and function

This area of research focuses on understanding of RNA folding into stable structures for a myriad of functions, such as modulating protein activities as drug candidates. RNA has extensive intramolecular interactions that cause it to fold from a linear molecule with specific sequence into an array of complex structures. RNA folding begins as the transcript is synthesized by RNA polymerase. The formation of RNA structures, such as hairpins, on the nascent transcript can create physical barriers that prevent backtracking and promote certain pathways favor specific tertiary structures with unique functional properties. Here we study the folding of an RNA, which can adopt multiple structures (not reversible, dynamic conformations) with distinct functions from transcription (i.e., copying of a single DNA sequence into RNAs by RNA polymerase).

An infographic with four images of liquid inside a test tube. The first image labeled “Hydrogel at room temp,” the second image labeled “Heated to 65 degrees Celsius,” the third image labeled “Cooled down to room temp” and the fourth image labeled “Lyophilized 2CZ hydrogel.” The infographic also includes two images of chemical compounds, one image of a test tube, two microscope images of motor neurons in mice, five line graphs and four microscopic images.

RNA: Hydrogel and biomaterials

Hydrogels are supramolecular assemblies with both solute transport properties like liquids and mechanical properties like elastomers. To date, every type of biomolecule — except RNA — is capable of forming hydrogel. Recently, we have found a unique RNA that can self-assemble, without any cross-linker or any external support matrix, to form hydrogel. In this case, a single RNA is the monomer, which contains proper recognition domains for intermolecular, non-covalent interactions in order to self-assemble into the hydrogel network structure. Hydrogels formed from biomolecules like RNA are generally biocompatible and can be chemically and biologically decorated and functionalized, making them particularly useful for tissue engineering and drug delivery, etc. We are identifying design modules and making various RNA hydrogels with different mechanical and physical properties. We are testing them using a variety of techniques such as SAXS, cryo-SEM and cryo-TEM.

A graphic showing multiple images, including four graphics and photos showing the implantation of Alzet Brain infusion set on rats/mice, a data graph illustrating latency to falls (percentage) and age (weeks), one image of immunostaining in mouse spinal cord, and two images of TDP-43 pathology in the motor neuron of AR2 mice.

Testing RNA aptamers with animal models of human diseases

Discovery of a drug candidate in terms of its efficacy and its potential toxicological effects requires in vivo study, and animal models are the most practical tools for in vivo, pre-clinical study of a drug candidate before its application in clinical trials. Currently, we are testing a group of RNA aptamers with two transgenic mouse models that mimic familial and sporadic ALS. ALS is a fatal type of motor neuron disease, and currently there is no cure. In one of our studies, for example, we examined the efficacy of an aptamer infused through intraventricular injection on mice with dysregulated AMPA receptor activity. We found that administration of the aptamer rescued both the number and the size of the motor neurons, and the mice performed better in motor function. We are also testing our RNA aptamers with a rat model that mimics neuropathic pain induced by spinal cord injury (SCI). Neuropathic pain caused by a lesion or disease of the somatosensory nervous system is a common chronic pain condition with major impact on quality of life. Most of the available treatments for neuropathic pain have moderate efficacy and present side effects that limit their use. Our preliminary study has shown that administration of RNA aptamers to rats with SCI has generated strong, long-lasting analgesic efficacy without any detectable side effects.

An infographic flowchart depicting computational modeling of RNA-glutamate receptor interactions. The title states Computational Screening methodology. The steps include: identify an RNA sequence, model the tertiary structure of RNA, dock the RNA with iGluRs, re-rank the complexes by a scoring system, generate the predicted complex structure and functional testing, before the steps begin again. There are also icons representing chemistry and RNA structures, and a photo of a lab assistant, included.

RNA-receptor molecular docking: Using computational approach for discovery of highly selective RNA aptamers

Computational modeling of RNA-glutamate receptor interactions has been a recent addition as a tool for our effort to develop RNA aptamers with high potency and selectivity. This method is especially useful when combined with RNA sequence mutations and then functional testing of the sequence variants with individual glutamate receptor channels using electrophysiology. The diagram below shows a flowchart of our approach.