Temple Univ Of The Commonwealth

NIH Research Projects · FY 2025 · 2017-05

Project Summary Understanding the conformational dynamics of proteins and their binding partners is crucial to predicting and designing their function. Molecular simulations are suitable for this task, but remain challenging for ligand binding systems where dissociation occurs on very slow time scales. We are developing new Markov state model (MSM) approaches, which describe conformational dynamics as a network of transitions between metastable states, to address this challenge. Multi-scale Markov models (MEMMs) offer a robust framework for building variationally optimal models of dynamics on long time scales, from ensembles of short trajectories sampled in biased thermodynamic ensembles, to predict ligand binding affinities, rates and mechanisms. During the coronavirus pandemic, our group used the distributed computing platform Folding@home (FAH) to perform virtual screening of SARS-CoV-2 main protease inhibitors by utilizing expanded-ensemble (EE) simulations, in which multiple alchemical intermediates can be sampled in a single simulation, to estimate binding free energies. This has inspired us to combine EE and MSM methods that can leverage the power of FAH to make fundamental advances in virtual screening and molecular design, in three specific aims: Our first aim is to improve EE methods for computing ligand binding free energies. In collaboration with the Shirts Lab, we seek to understand and ameliorate convergence issues, and explore and unify related approaches. We will investigate how well EE estimates of free energies of mutations can be used with MEMMs to predict changes in protein folding stability and rates. Finally, we will work with the Karanicolas Lab to determine the extent to which EE-calculated ABFEs on FAH can be used alongside advanced machine learning classifiers to discover both active and potent inhibitors from structure-based virtual screening studies. Our second aim is to develop a combined metadynamics (metaD) + MEMM approach for modeling binding reactions. We will develop and test two different strategies in which metaD is used to derive negative potentials of mean force along binding reaction coordinates that can be used as bias potentials for constructing multi- ensemble Markov models (MEMMs) of ligand binding. We will test these methods in toy binding systems, and small ligands of L99A lysozyme. Finally, we will apply metaD+MEMMs to predict affinities, rates and mechanisms of the macrolide natural product carolacton binding to FolD and its known drug-resistant mutants. Our third aim is to examine the extent to which solution-state preorganization determines binding affinity, and whether simulation-based modeling can use this idea quantitatively for computational design. For a corpus of 105 cyclic peptides with published affinities, EE+MSM approaches will test the validity of a two-step conformational selection model. The results of this work will guide the design, testing and optimization of cyclic peptide binders to disrupt dimerization of the tumor suppressor PTEN, a collaboration with the Rongsheng Wang Lab at Temple, to find new diagnostics/therapeutics for cancer metastasis.

NIH Research Projects · FY 2025 · 2015-09

Project Summary The long-term goal of this project is to define molecular mechanisms that govern the long distance transfer of protein-based signals in axons. Retrograde (axon-to-soma) signals are critical to activate transcriptional programs both during neurodevelopment and following nerve injury, while continuous anterograde (soma-to- axon) supply of `axon survival factors' is essential to maintain distal axon integrity. We and others have found that key proteins that convey these retrograde and anterograde signals are modified with the lipid palmitate, which facilitates their trafficking on axonal vesicles. In particular, experiments in the first cycle of funding revealed that retrograde signaling by Dual Leucine-zipper Kinase (DLK, an upstream activator (a `MAP3K') of Mitogen-activated Protein Kinase (MAPK) pathways) critically requires palmitoylation. We now hypothesize that palmitoylation more broadly controls several distinct aspects of axonal signaling. The first Aim will focus on palmitoylation of JNK family MAPKs, which are key `effector' kinases downstream of DLK and other MAP3Ks. We will determine whether palmitoylation of the neural-specific JNK3 is required for Wallerian degeneration of distal axons, and whether JNK3 phosphorylates palmitoylated axon survival factors, triggering their degradation via a novel phospho-dependent mechanism. Aim 2 will focus on Rap2, a novel palmitoylated regulator that lies upstream of DLK, and will determine whether Rap2 and its palmitoylation are broadly required for DLK-dependent retrograde signaling. Aim 3 will assess whether the unique reversibility of palmitoylation, compared with other protein-lipid modifications, is used to facilitate `sushi belt transport' whereby the key axon survival factor NMNAT2 undergoes palmitoylation-dependent anterograde trafficking on vesicles and is then locally depalmitoylated to increase its enzymatic and axo-protective activity. The proposed research will define new cellular and molecular roles for palmitoylation in axonal protein trafficking and signaling and will provide key insights into how responses to axonal damage are coordinated and controlled. Results of our study may also reveal broader principles of axonal protein transport and signaling, in turn increasing our understanding of a range of neurodegenerative disorders in which these processes are impaired.

NIH Research Projects · FY 2026 · 2014-02

Project Summary / Abstract Dementia is a daunting public health crisis facing many industrialized nations. A key component of the global action plan for dementia proposed by the World Health Organization (WHO) involves early detection and the development of novel therapeutics.1 There exist great racial and socioeconomic barriers to dementia care in the United States. Many existing neuropsychological measures lack sensitivity to accurately screen for dementia in under-represented minority populations. During the next project period, we will focus on early detection of emerging semantic deficits in naturalistic language samples. Our focus is on changes in language cognition, and physiology of the pupil response function among a cohort of older African American adults at elevated risk for dementia. We will derive age-based norms for language content during narrative production and evoked pupillary dynamics (e.g., speed of pupil dilation) during both the production and perception of language. Our studies will elucidate the relationship between changes in executive functioning and semantic knowledge over the span of five years in a radically underserved population.

NIH Research Projects · FY 2025 · 2013-01

Project Summary The overarching goal of the proposed research is to predict the intracellular and extracellular concentration- time profiles using models that include membrane partitioning, membrane permeability, organ blood flow, active transport, and metabolism. In the funding period from 2018-2022, we have made significant progress in developing models to predict drug volume of distribution, and models to predict drug absorption. We have used the basic principles underlying permeability and partitioning to build a new framework for PBPK models (termed PermQ). This framework now allows us to incorporate permeability-limited distribution, partitioning, organ blood flow, and active transport into PBPK models with explicit membrane kinetics. We have started to build upon our current work to develop novel frameworks to predict drug clearance, a new focus of this renewal. These new modeling paradigms, together with our time- and distance- dependent continuous absorption models, will provide markedly better predictions of intracellular concentrations in the presence of drug metabolizing enzymes and transporters, and will address an unmet critical need for cost effective drug development by providing novel predictive tools for drug pharmacokinetics in humans. Three specific aims are proposed. 1) New in vitro and mathematical methods will characterize the time-course of cellular permeability and partitioning, to inform mechanisms underlying drug distribution, absorption, and intracellular concentrations that drive drug clearance. Experiments in artificial membrane environments at various pH values will define the pH partitioning – membrane permeability relationship. In vitro microdialysis and transwell techniques will capture the time-course of drug partitioning into cells including MDCK, Caco-2, adipocytes, and hepatocytes. Partitioning into erythrocyte glycocalyx will be measured. Resulting data will be used as inputs to develop mathematical models to predict drug permeability across single vs. multiple membranes across a cell, and drug partitioning into membranes. 2) Excipient effects on oral absorption will be predicted in humans and rodents. Effect of excipient dose-dependent (Polysorbate 80 and PEG400) inhibition of intestinal drug metabolizing enzymes and transporters (DMETs) will be evaluated with a refined rat intestinal model. A continuous intestinal mouse absorption model will be developed and refined. The human and rat intestinal models will be interfaced with species-specific PermQ models. 3) New in vitro and mathematical methods will improve predictions of drug clearance. Rat data will be collected with microfluidics in hepatocytes and in vivo, with regional drug quantification with MALDI imaging. Three standard liver models – well-stirred (WSM), parallel-tube (PTM), and dispersion (DM) – will be evaluated within human and rat PermQ. Enzyme zonation within the liver sinusoid will be modeled with both literature (discretized) and new partial differential equation (continuous) methods.

NIH Research Projects · FY 2025 · 2011-08

SUMMARY Current treatment of HIV-1 infection has changed the face of the disease by converting a once acute deadly disease to a chronic illness. As such, many other issues have surfaced that require close attention including comorbidities associated with the presence of the viral genome, as well as the potential side effects of ART on several tissues and cells including brain that impact on the homeostasis of neuronal cells thus contributing to neurocognitive and behavioral disorders seen among people living with HIV (PWH). Other areas of concern relate to social and structural determinants of NeuroHIV disparities in the PWH community. Now, it has become increasingly clear that the landscape must move toward a cure by employing sophisticated, innovative, next generation approaches and technologies that are aimed at the permanent elimination of HIV-1 in PWH and protect uninfected individuals from HIV-1 infection at the cellular and molecular levels. Importantly, a parallel approach to improve neurocognitive/psychological disorders in the HIV community as well as the use of molecular strategies for elimination/protection must be implemented to end more than four decades of clinical challenges caused by HIV-1 infection. By combining resources and expertise of our teams at Temple and Drexel, we have developed a Comprehensive NeuroHIV Center (CNHC) facility to provide services to scientists from the greater Philadelphia area and beyond to initiate and investigate the current issues associated with neuroscience of HIV-1 from community to laboratory and clinic with an emphasis on neuropsychiatric/behavioral (a new area of emphasis), continued studies on the neuroscience of HIV-1 infection, and the development of cure strategies at the molecular and cellular levels by the elimination of HIV-1 proviral DNA from the host using a genetic approach such as CRISPR gene editing-based technologies. We propose that this unique and unprecedented strategy will have dual benefit in improving current challenges associated with HIV-1 infection in PWH community and offer new opportunities for the development of a novel approach for mitigation/elimination of viral infection by a highly collaborative and complementary group of scientists. Our goals remain to provide neuroHIV research infrastructure and support utilizing and expanding the CNHC's rich clinical neuropsychological data from a longitudinal cohort of PWH, including primarily Black/African-American and White participants that identify as non-Hispanic or Hispanic origin well-characterized by deep sequencing and detailed immunophenotyping as described in the Clinical and Translational Research Support Core (CTRSC), working closely with NeuroHIV Community Partnership and Disparities Core (NHCPDC) and taking advantage of the expert services offered by Viral Gene Editing and Bioinformatics Core (VGEBC), together with resources offered by the Cell Biology and Functional Analysis Core (CBFAC), and the financial and intellectual opportunities offered by the Developmental Research and Mentorship Core (DRMC). All of which are operationally optimized and orchestrated by the Central Administrative and Management Core (CAMC) to maximize our achievements.

NIH Research Projects · FY 2024 · 2010-05

Abstract: The animal studies in this renewal application will parallel the clinical trial studies to further understand the mechanisms of somatic reinnervation for restoration of bladder emptying function. Aim 1: Address the following questions: • Will administration of growth factors into the reinnervated urinary bladder wall improve recovery? • Which are the most effective growth factors to use? Will it be: a) Factors produced by the decentralized bladder cells (smooth muscle, intramural ganglia, interstitial, urothelial cells), b) Factors that promote neonatal survival of bladder spinal motoneurons; or, c) Factors that optimally attract the somatic motor fibers from the donor obturator nerve? • What growth factors promote functionally optimal afferent reinnervation? Aim 2: Address the following questions: • Is the one anterior vesical branch of the pelvic nerve on each side that is reinnervated by a portion of the obturator nerve branch sufficient to achieve effective bladder emptying and sensation? • Is the loss of innervation from transecting vesical branches alone enough to result in loss of bladder function or this there sufficiently retained innervation through other branches such that the voiding function recovers with time? • Is the recovery of voiding behavior truly the result of the new neural pathway from the nerve transfer or some other spontaneous recovery? • Will obturator to anterior branch of the pelvic nerve transfer performed before decentralization improve recovery of bladder function? Aim 3: Answer the following questions using the canine tissue bank accrued from the previous funding cycles and from the new animals in these proposed studies: • What properties have changed in the axotomized motor nerves and how are these altered by rerouting? • What types of efferent fibers are reinnervating the bladder from the obturator nerve and on what type of cells do these new fibers terminate? • Do the new bladder efferent fibers originate from the ventral horn, sympathetic chain ganglia or both? • What types of afferent fibers are growing into the bladder from the obturator nerve and what are their en- organ targets? Is it urothelium, intramural ganglia, muscles, or blood vessels?

NIH Research Projects · FY 2025 · 2009-07

Repetitive overuse induced musculoskeletal injuries (MSKls) are the leading cause of pain and physical disability worldwide, Treatment has proved difficult We believe that 4 issues underlie this problem - (1) the frequent, yet incorrect, assumption that occupational physical activity is as equally beneficial as voluntary exercise; (2) a failure to consider how pathological processes vary and interact over time; (3) underinvestigation of sex-linked differences and consequences of aging ("inflammaging" and reduced repair); and (4) overlooking what we hypothesize are key factors involved in the transition to chronicity, e,g,, poor sleep and fibrotic/degenerative processes, It is time to take a fresh approach to reduce the enormous burden of MSKls, One promising, non-pharmacological alternative is improved sleep, since poor sleep generates a systemic inflammatory response and lowers one's tolerance and threshold to painful stimuli, Another efficacious nonpharmacological intervention for MSKI pain is whole body aerobic exercise, Although the pain-relieving mechanisms of whole body general exercise remain unclear, evidence points to its capacity to lower systemic inflammation, Additionally, since idiopathic tendinopathies and compressive mononeuropathies are associated with increased pain and weakness, we hypothesize that tissue fibrosis is a key factor in the dysfunction with chronic overuse MSKls, Although recovery from tissue fibrosis is typically thought to be slow or irreversible, we found that early treatment with novel anti-fibrotic agents, including anti-CTGF/CCN2 (anti-connective tissue growth factor/cell communication network factor 2, called FG-3019), reduced developing nerve and musculotendinous fibrosis, and remarkably reversed established widespread fibrosis and restored tissue structure and function in our rat model of overuse injuries, Aim 1, we will determine in young adult rats (3 mo of age at onset), using our operant model of overuse injuries: (a) causal pathways in overuse MSKls, focusing on roles of poor sleep, tissue inflammation and fibrosis; (b) whether sleep has a role in moderating pain intensity/persistence; and (c) whether undisturbed sleep or whole body exercise, and reduced fibrosis using FG-3019, or a combination, effectively improves function and reduces pain, Aim 2, will be similar, except we will use very mature rats (15 mo of age), We hypothesize that poor sleep, low physical activity, psychological factors, and specific systemic inflammatory and fibrotic profiles, will increase the risk of pain and be predictive of poor recovery, We further hypothesize that in combination, improved sleep and general whole body exercise could have a cumulative anti-inflammation effect, and by impacting numerous bodily systems, Furthermore, if tissue fibrosis is also reduced, we hypothesize an acceleration of recovery and restoration of neuromusculoskeletal function, Results are expected to provide new insight into causal pathways of chronic overuse MSKls; how disruption of normal sleep adversely affects outcomes from injury, and pathways through which exercise positively impacts pain; and how aging influences these responses,

NIH Research Projects · FY 2024 · 2008-09

The purpose of our program is to provide a broad-based, multidisciplinary training experience for pre-doctoral fellows, postdoctoral fellows, and summer medical students in the area of integrative cardiovascular pathophysiology (ICVP). ICVP faculty members are affiliated with various basic science and clinical departments, with research laboratories primarily located within the Department of Cardiovascular Sciences, housed on two adjacent floors of a new medical research building. ICVP investigators and mentors have shared interests in the fundamental properties of the cardiovascular system and the pathological changes that contribute to cardiovascular dysfunction in diseases such as ischemic heart disease, hypertensive heart disease, atherosclerosis, ischemic vascular disease, metabolic syndrome, and diabetic cardiovascular disease. Graduate students and postdoctoral fellows will receive didactic training in human physiology and pathophysiology, along with advanced instruction in cellular and molecular biology and the appropriate use of animal models of human cardiovascular disease. Research projects for graduate students and fellows will include both basic and translational components. Trainees will be encouraged to investigate problems that extend beyond single-molecule studies, addressing complex questions within the broader context of cardiovascular disease models. Portions of these projects will be conducted in the laboratories of multiple investigators, providing trainees with exposure to diverse scientific approaches. All trainees will participate in activities designed to strengthen their grant writing, manuscript preparation, and oral communication skills. Group mentoring by both junior and senior faculty will ensure that trainees are well prepared to become leading investigators capable of rapidly translating new scientific knowledge into novel therapies or therapeutic targets. Recruitment strategies will focus on attracting highly qualified candidates with the potential to contribute meaningfully to the advancement of cardiovascular science. The overarching goal is to train the next generation of biomedical scientists who are equipped to develop innovative therapies for cardiovascular disease.

NIH Research Projects · FY 2025 · 2008-07

ABSTRACT This renewal application requests support for the continuation and further development of the “Interdisciplinary and Translational Research Training Program (ITRTP) in NeuroHIV” for predoctoral students studying central nervous system (CNS) complications of HIV infection and related areas of research. HIV-associated neurological disorders represent a complex disease requiring an integrated multidisciplinary approach designed to effectively train future research leaders in the field. This program brings together multiple biomedical basic science departments across Colleges/Schools at both Temple and Drexel and integrates joint training activities at these two neighboring institutions (Temple and Drexel) with unique and long-standing relationships between investigators located at the University of Pennsylvania (Penn) with all institutions located in close proximity in Philadelphia, PA. In addition, this program integrates training activities and research resources available in our NIMH-funded Comprehensive Center for NeuroHIV (CNHC) involving both Temple and Drexel University and the Penn Center for AIDS Research (CFAR). Inclusion of access to clinical HIV investigators in translational student research projects, as well Temple/Drexel CNHC basic science and clinical core facilities greatly enhances the NeuroHIV ITRTP with respect to its interdisciplinary nature. It also exposes students to the interrelatedness of basic sciences and clinical/translational perspectives focusing on HIV-induced CNS dysfunction, co-morbid conditions (i.e., aging, substance abuse, co-infecting pathogens, and cancer), HIV vaccine and prevention strategies, and novel neuroprotective and therapeutic strategies to treat and cure HIV infection in the periphery and reservoirs, including the brain. Our joint training program, together with our joint infrastructural resources available through our CNHC, provides a strong, interactive, and highly successful training environment in neurovirology and neuroHIV within the Philadelphia region. Our ongoing program will continue to develop our citywide ITRTP in NeuroHIV through shared resources, joint seminars, workshops, symposia, as well as thesis mentoring and educational activities available at both Temple and Drexel. The graduate curriculum at both institutions is designed to provide a broad-based scientific foundation in biomedical sciences, including neuroscience, immunology, microbiology, pharmacology, engineering, and physiology. The training program consists of integrative sessions, including seminars, didactic lectures, and clinical content, all focused on NeuroHIV. The curriculum also includes responsible conduct of research, scientific communication, statistics, as well as advanced courses with in-depth training in molecular and cellular neurobiology, neuropathogenesis, and translational neuroscience that has proven to be effective and productive.

NIH Research Projects · FY 2025 · 2006-04

PROJECT SUMMARY Patients with gastroparesis often suffer with chronic symptoms that are not adequately treated due to both a lack of understanding of the underlying pathophysiology of gastroparesis and lack of effective treatments. Participation of Temple University as a clinical center in the NIDDK Gastroparesis Clinical Research Consortium (GpCRC) and Temple's proposed studies will help achieve the broad, long term objectives of improving the understanding and treatment of patients with gastroparesis. The PI and Temple University are well qualified to continue to be one of the clinical centers in the GpCRC. Temple University has extensive clinical expertise in gastroparesis and has been active in study development, enrolling patients into studies, manuscript publication, and obtaining funding for ancillary studies. The aims for Temple's renewal for the GpCRC are threefold. First, to continue enrollment and follow-up of patients in current GpCRC studies: GpR3, BESST, PBG, PSAG. We will maintain the Gastroparesis Registry 3 (GpR3) to enroll 400 patients with follow- up on patients for 1 to 4 years. GpR3 was recently enhanced to study the effects of SARS-CoV-2 in patients with gastroparesis. We continue to enroll in the clinical trial Buspirone for Early Satiety and Symptoms of Gastroparesis (BESST). Our Pathological Basis of Gastroparesis (PBG) is studying immune cell profiles in gastroparesis. We will start our study on pyloric pathophysiology: Pyloric Sphincter Abnormalities in Patients with Gastroparesis Symptoms (PSAGS). Second, to better understand the clinical manifestations and pathophysiology of patients with symptoms of gastroparesis, we will start a new registry, Gastroparesis Registry 4 for enrollment of 400 new patients. This application includes suggestions for five areas of study: 1) evaluating for autoimmune gastroparesis; 2) understanding meal eating characteristics and ARFID-like symptoms in patients with gastroparesis; 3) assess for hypocortisolism which can occur in gastroparesis patients and add to the symptom severity; 4) assessing for vagal and peripheral neuropathy as pathophysiologic comorbidities in gastroparesis; and 5) further enhancement of gastric emptying scintigraphy (GES) assessing antral synchronicity and antropyloroduodenal coordination. Third, to conduct a new multicenter study investigating the pathophysiology, diagnosis, and treatment of gastroparesis. Our application proposes a new study, Relating Gastric Pathophysiology using GES with DACS to Treatment Outcome, aimed at understanding the pathophysiologic basis of gastroparesis and its relationship to symptoms. The goal is to better target specific treatment based on pathophysiology and symptoms. Temple's participation and proposed studies will help achieve the goal of the NIDDK GpCRC to advance our understanding and treatment of gastroparesis.

NIH Research Projects · FY 2025 · 1988-09

Diseases of addiction and related drug overdose deaths remain a major public health problem of the United States. Addressing these challenges and discovering innovative solutions requires a workforce specifically trained for this purpose. This renewal application is requesting the continuation of the ‘Neurobiology of Addiction Training Program’ at Temple University (T32 DA007237) which has served as the cornerstone for interdisciplinary training in the basic science of addiction since 1988. Its successes can be seen by the number of highly trained, productive scientists that have joined the workforce and the dissemination of impactful research findings through their peer-reviewed publications. The Training Program is administered under the auspices of the Center for Substance Abuse Research (CSAR) at the Lewis Katz School of Medicine at Temple. CSAR brings together faculty from many disciplines who share a passion for uncovering the neurobiology of addiction, the pharmacology of drugs of abuse, and the intersection of drugs with immune function including HIV. This common goal creates a rich, highly collaborative environment that is ideal for mentoring the next generation of scientists whose research often extends beyond a single laboratory or discipline. Temple’s institutional support for training, research and treatment in the area of substance use disorders has never been higher, as exemplified by the recent investment in the recruitment of additional faculty and the creation of the new Temple Institute for Addiction Research and Medicine. The program’s priorities include fostering training and scientific innovation, establishing collaborations and connections, instilling personal and public accountability in the conduct of science, and supporting a dynamic training environment. Students come from four graduate programs in three colleges across the university: the medical school’s Biomedical Sciences graduate and MD/PhD programs, and the PhD programs in Psychology and Pharmaceutical Sciences. Trainees are mentored by 21 faculty who conduct research related to the neurobiological basis of addiction or the intersection of drugs and HIV. Temple’s NIDA Training Program has excelled in recruiting outstanding trainees and boasts a near perfect retention rate. Trainees complete the program with excellent credentials and pursue successful careers in academia, industry, government and other science-related fields, thus fulfilling the NIH’s directive to improve human health. This Training Program is a vital resource for supporting students and postdoctoral fellows and advancing the field of addiction research.