Lab Members

Sara Jackson

Ph.D. Student

Bio

Sara Jackson is a PhD student in the Biotechnology Science and Engineering (BSE) program.

She received a BS degree in Cell and Molecular Biology from Troy University, where she conducted undergraduate research under the mentorship of Dr. Philip Reynolds on heat shock proteins and androgen receptor function. She then received a MS degree in Biomedical Science from Florida State University, working in Dr. Mike Blaber’s lab on the role of kallikrein proteases in multiple sclerosis etiology. Work experience in commercial and clinical labs precede her enrollment in the BSE program at UAH. Sara is interested in computationally exploring protein architecture and function to answer biological questions. Current research in the Baudry lab includes quantum mechanical characterization of a small molecule enzyme mediator, informing identification of lead compounds via molecular docking, and building on T cell receptor work from Dr. Joe Ng’s lab with molecular dynamics simulations of large-scale protein-protein interactions.



Current research:

T cell receptor (TCR) alpha (pink) and beta (cyan) chains from PDB structure 6JXR. The hypervariable CDR3 loop of the beta chain with mutations is highlighted in red.

An ensemble of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complexes prepared for ligand docking from molecular dynamics trajectory clustering. RdRp in magenta; RNA in cyan.

Maher Mansur

Ph.D. Student

Bio

Maher Mansur is from Chittagong, Bangladesh. He completed his bachelor's and master's degrees in microbiology from the University of Chittagong. Following that, he gained professional experience in the pharmaceutical industry in Bangladesh for one and a half years. He has training in diverse fields of biology and chemistry. His research interests are using computational methods for protein modeling & design and drug discovery. In the Baudry Lab, he leads several projects on rare developmental disorders, viral proteins, and cytochrome P450 enzymes. For the latter, he received the Chateaubriand Fellowship from the Embassy of France in the United States. He is a recipient of the ORISE Fellowship and has joined the Research participation program at the NCTR-FDA. He is a part of an interdisciplinary team on a study to monitor and evaluate mutations of SARS-CoV-2, and their impact on FDA Approved diagnostics, vaccines, and therapeutics.


Current research:


Maher Mansur is working on projects involving proteins playing roles in human development, viral infection, and chemical oxidation of environmental pollutants.

Armin Ahmadi

Ph.D. Student

Bio

Armin Ahmadi received both his BSc in Chemical Engineering and MSc in Chemical & Bioengineering from Sharif University of Technology, Tehran, Iran. Followed by receiving an MSE in Chemical Engineering, he continued his PhD studies in Mechanical Engineering at the University of Alabama in Huntsville.

Current research:

Armin's research at Baudry lab is about Ensemble Pharmacophore Generation to Enhance large-scale Virtual Screening and Drug Discovery.

Boshra Rezvanian

Ph.D. Student

Bio

Boshra Rezvanian is from Tehran, Iran. She completed his master's degree in Chemical Engineering with concentration in Pharmaceutical Engineering from the University of Tehran. She started working with Dr. Jerome Baudry at The University of Alabama Huntsville to pursue a PhD in Biotechnology in 2021. Her research interests are focused on using computational methods for protein modeling & design and drug discovery.

Current research:

In the Baudry Lab, Boshra Rezvanian is leading several projects on rare Pediatric disorders and modeling transmembrane proteins.

Poshan Pokharel

M.S. Student

Bio

I am from Kathmandu, Nepal. I completed my bachelor’s degree in Health Science and a minor in Computer Science from Athens State University, Athens, Alabama. I did clinical research on Amyotrophic Lateral Sclerosis at Crestwood Medical Center for a year before starting my further studies at UAH. I am currently working on my master’s program in biological sciences here at the University of Alabama in Huntsville. Parkinson’s disease (PD) is the second most common neurodegenerative disorder in the world. There are treatments available for the disorder, but the treatments do not prevent the progressive neurodegeneration. P75NTR is a transmembrane protein that has been demonstrated to regulate the survival of specific populations of neurons affected by various pathological conditions, as well as in models of Alzheimer’s disease and amyotrophic lateral sclerosis.

Current research:

Poshan is currently working with Dr. Baudry to determine the structure of p75NTR and design a ligand to inhibit its cleavage by ADAM17 (TACE) and gamma-secretase, and furthermore inhibiting its downstream signaling which leads to neuronal death

Email : mh0211@uah.edu

Manasa Nagesh Hegde

Ph.D. Student

Bio

Manasa is from Karnataka, India. She completed her bachelor's and master's degrees in Biotechnology from Visvesvaraya Technological University, India. Following that, she worked as a Junior Research Fellow at the UNESCO-Regional Center for Biotechnology(RCB), Faridabad, India before joining UAH in fall 2021 for Ph.D in Biotechnology Science and Engineering program. Her research interests are drug discovery, ligand-protein interactions and molecular docking.

Current research:

Terpenes are the naturally occuring, most diverse and largest group of naturally occurring compounds, which are mostly present in plants. Terpenes provide medical benefits in the form of drugs, and play a variety of roles such as antibacterial, anti-oxidant, and anti-inflammatory roles. Manasa is currently working in Dr. Baudry’s lab to identify the target proteins that terpenes bind to, and search for beneficial interactions in order to utilize them as drugs.

Emika Miyamoto

M.S. Student

Bio

Emika grew up in the huntsville area and completed her bachelor's degree in Biology at UAH with a minor in chemistry. She is working on her masters degree and is currently using data clustering methods on Molecular Dynamics trajectory datasets of GPCRs to find a way to reliably distinguish protein conformations that are more successful in binding to its known active ligands among the less successful conformations.

Current research:

Without knowledge of a protein’s ligands, it is currently not known how to predict the structures that will bind successfully to potential drug candidates. Her research at the Baudry Lab aims to gain a better understanding of conformationally selected structures through data clustering in hopes of overcoming this problem and finding a method that can be used to cut down on the time, cost, and failure rate of the drug discovery process.

Undergraduate Researchers

Alumni

Meredyth Kinsella

M.S. Student

Bio

Meredyth is a Huntsville native who first attended the University of Montevallo for fine arts with a concentration in illustration and 2D design. Mid-degree she fell in love with the biological science and transferred to UAH to pursue bachelors degrees in Biology and Chemistry with a concentration in Biochemistry. Meredyth hopes to use her passion for problem-solving and her knowledge of biological systems and chemistry to research new methods of drug discovery and delivery


Current research:


Meredyth Kinsella is working towards understanding the enzymatic mechanism of bacterial Pth1 and finding an inhibitor.

P. aeruginosa peptidyl-tRNA hydrolase (Pth1) - PDB ID 4FYJ

Jay Spencer

Ph.D. Student

Bio

Jay Spencer is originally from Sevierville, TN. He completed a baccalaureate degree in biological sciences with a concentration in Biochemistry Cellular and Molecular Biology from the University of Tennessee Knoxville (‘17). Upon graduation, he followed his undergraduate advisor, Dr. Jerome Baudry to The University of Alabama Huntsville to pursue a Ph.D in Biotechnology, with a concentration in computational biology. He is currently funded through an R01 grant to develop a group A strep vaccine targeting the M protein using molecular dynamics and in silico epitope prediction.


Current research:


Jay Spencer is currently working towards a group A strep vaccine.


Electrostatic surface map of the N-terminus of M3, a GAS serotype commonly linked to rheumatic heart disease.

Dr. Anna Petroff

Baudry Lab PhD Graduate 2021

Bio

Dr. Anna Petroff was awarded a PhD in June of 2021, making her the first PhD graduate of the UAH Baudry Lab. Sincere thanks to the Mrs. Pei-Ling Chan Endowment.

Prior to completing a PhD in Biotechnology Science and Engineering, Dr. Petroff completed degrees at Warren Wilson College in Asheville, NC (B.A. English Literature Hon.) and Appalachian State University in Boone (M.A. Experimental Health Psychology). Her overarching research interest is to explore the actions of proteins implicated in the development and persistence of psychological disorders. Her interdisciplinary background has afforded her a range of experiences, from clinical experiments to molecular modeling of membrane proteins.


Current research:


Anna Petroff is currently researching membrane-bound desaturases using all-atom molecular dynamics.


The figure above shows a model of stearoyl-CoA desaturase (red) in a membrane (magenta) with substrate (yellow).

Dr. Kendall Byler

Researcher

Bio

Kendall Byler is a research associate in computational chemistry/biology in the biology department. He began his education at The University of Alabama in Huntsville, receiving both a B.S. in chemistry, focusing on natural products, and an M.S. in chemistry, focusing on ab initio calculations of DNA-intercalator interactions, followed by doctoral studies at the Computer Chemie Centrum in computational chemistry (3D-QSAR) at Erlangen, Germany. This was followed by postdoctoral appointments at The University of British Columbia, Mayo Clinic and Torrey Pines Institute for Molecular Studies. Kendall also began teaching chemistry at Indian River State College, and later returned to UAH to teach general and organic chemistry as a lecturer in the chemistry department while continuing independent research in improving molecular docking methods for the identification of natural product structures active in targets in neglected tropical diseases, such as Zika virus, in association with ResNet NPND. His experience in computational chemistry ranges from ab initio transition state calculations to quantitative structure activity/property modeling using machine learning to molecular docking and molecular dynamics simulations of ligand-receptor interactions of biological systems associated with disease states.


Current research:

Dr. Byler is investigating the prediction of tissue-specific cytochrome P450 metabolites of xenobiotics and harmful tobacco product components using structure-based techniques

The structure of indole bound to the heme group of human lung CYP2A13.

Amy Ridings

M.S. Student

Bio

Although she grew up in southern California, Amy Ridings has called the South her home since 2005. She attended Middle Tennessee State University where she graduated with a bachelor’s degree in Biological Sciences from the Honors College. From there, she went to Tennessee Technological University, where she studied computational chemistry, and earned her master's degree in Chemistry in May 2019. Her research interests are rooted in drug discovery, natural products, especially those from Traditional Chinese herbal medicine, and molecular modeling.

Amy Ridings studied the dynamics of PCSK9.


Model of PCSK9 structure solvated in an explicit periodic water box for all-atom molecular dynamics simulation.

Jana Whittle

M.S. Student

Bio

Jana Whittle is native of Huntsville. She started her undergraduate work at UAH and then completed her BS degree at UAB in mathematics with a concentration in statistics. Jana worked as a software developer in the private sector for over 12 years, specializing in user-interface design. Following this work, Jana returned to school at UAH for a degree in Biotechnology. She wants to explore biological questions using computational and big data methods.




Jana Whittle worked to develop methods to computationally determine favorably bound ligands based on descriptors of protein conformation properties.


The figure above shows the binding pocket of GPCR protein ADORA2A.

Dr. Noriko Inoguchi

Post-Doc

Bio

Dr. Inoguchi is a postdoctoral research assistant originally from Japan. She completed her bachelor's degree in Interdisciplinary studies in Science and Math at Southeast Missouri State University (Cape Girardeau, MO) and worked as a student researcher for 3 years during the undergraduate period mentored by Dr. Walt Lilly and Dr. Allen Gathman. She received her Ph.D. in Biological Sciences with emphasizing X-ray protein crystallography at University of Nebraska-Lincoln (Lincoln, NE) under the supervision of Dr. Hideaki Moriyama. She started her postdoctoral research at iXpressGenes, Inc. at HudsonAlpha Institute for Biotechnology (Huntsville, AL) focusing on neutron crystallography with Dr. Joseph Ng as a supervisor, then moved to University of Alabama in Huntsville to work on computational biophysics with continue working on protein biochemistry and X-ray/neutron protein crystallography with Dr. Ng.




Dr. Inoguchi worked on deciphering the molecular mechanism of Thermococcus IPPase by crystallography and molecular dynamics.

Water-network identified by neutron crystal structure (PDBID: 5TY5)

Kyrie Chandler

Kyrie is interested in the molecular interactions and regulation between proteins, ligands, and DNA. She is currently working to identify potential proteins that can be targeted for anti-inflammatory drug development. The ConceptalEyes semantic search program, which is a form of A.I., facilitates identification of potential proteins that may interact with active organic molecules isolated from certain plant extracts. The objective is to create a matched list of protein targets, active molecules, and diseases that can speed the process of drug discovery. Kyrie plans to pursue a PhD to apply bioinformatics to the rapidly developing field of Regenerative Medicine.


Shayenne Arehart

Shayenne is a pre-med student aspiring to be a psychiatrist. She has a strong interest in pharmacology, especially psychopharmacology. In Dr. Baudry's lab, Shayenne is computationally mapping mutations that render a specific enzyme dysfunctional and contribute to the genetic disorder tyrosinemia type 1 (TT1). TT1 is a disorder in which the patient is unable to efficiently break down tyrosine due to a defect in the enzyme fumarylacetoacetate hydrolase. Patients with this condition may present with developmental delays, and understanding the biological basis of this genetic disorder grants medical professionals the potential to develop improved treatment for affected patients, including psychiatric and pharmaceutical treatments.

Corinne Peacher

Corinne is currently pursuing a bachelor’s degree in biological sciences with a minor in computer science. She has a strong interest in data science and computational biology. Working under Dr. Menon and Dr. Baudry, Corinne analyzes biomedical datasets on G-protein coupled receptors (GPCRs) and uses this data to train machine learning algorithms to help identify active bindings between drug candidates and the target protein. GPCRs are a large family of integral membrane proteins that regulate most of a human's physiological responses to hormones, neurotransmitters, and environmental stimulants, making GPCRs ideal for target proteins in the drug discovery and development process. The main objective of her work is to develop a method that can overcome the class imbalance problem that is often found in biomedical datasets in order to maximize the predication rate of drug-candidates for target proteins.

Interested in joining us?

The Baudry Lab is actively recruiting highly motivated M.S. and Ph. D students.