Chemicals and Drugs Commons^™

First-Generation Cephalosporins For Treatment Of Acute Hematogenous Osteomyelitis In Children: A Study Of Efficacy And Adverse Effects, Lisa Hiskey, Hiba Saifuddin, Emily R. Levy, Roland Hentz, Nipunie S. Rajapakse, Laura M. Dinnes, Elizabeth H. Ristagno

School of Medicine Faculty Publications

BACKGROUND: Acute hematogenous osteomyelitis (AHO) is a relatively infrequent but significant infection in pediatric patients. As is the most common cause of AHO, intravenous and oral first-generation cephalosporins are common therapies. Cephalexin is a commonly prescribed oral therapy for pediatric AHO, although it requires frequent dosing that may affect adherence. Cefadroxil is a comparable oral first-generation cephalosporin with a more desirable dosing schedule. METHODS: We reviewed pediatric patients admitted to Mayo Clinic between March 2002 and September 2020 for management of AHO who received treatment with a first-generation cephalosporin. We reviewed timing of oral therapy transition, therapy-associated adverse effects, and …

Utilization Of Semiconductor Nanocrystals In Cancer Diagnose And Treatment, Yasir Q. Almajidi, Ahmed A. Albadri, Mazen M. Jwaid, Yaseen T. Khalaf

Maaen Journal for Medical Sciences

In contemporary times, nanotechnology has emerged as a notably sophisticated technological discipline. It possesses an interdisciplinary and multidisciplinary nature, spanning a wide array of domains including medical science, engineering, biology, physics, materials science, and chemistry. Utilization of nanotechnology offers a significant advantage by enabling precise manipulation and control of properties to effectively address specific challenges in various applications. In the fields of science and biomedicine, there has been extensive exploration into the use of functional nanomaterials, emerging as rapidly advancing and captivating areas of research. Diverse types of nanomaterials, including silicon nanowires, quantum dots, carbon nanotubes, and gold/silver nanoparticles, which …

Elovanoid-N34 Modulates Txnrd1 Key In Protection Against Oxidative Stress-Related Diseases, Jorgelina M. Calandria, Surjyadipta Bhattacharjee, Sayantani Kala-Bhattacharjee, Pranab K. Mukherjee, Yuehan Feng, Jakob Vowinckel, Tobias Treiber, Nicolas G. Bazan

School of Graduate Studies Faculty Publications

The thioredoxin (TXN) system is an NADPH + H+/FAD redox-triggered effector that sustains homeostasis, bioenergetics, detoxifying drug networks, and cell survival in oxidative stress-related diseases. Elovanoid (ELV)-N34 is an endogenously formed lipid mediator in neural cells from omega-3 fatty acid precursors that modulate neuroinflammation and senescence gene programming when reduction-oxidation (redox) homeostasis is disrupted, enhancing cell survival. Limited proteolysis (LiP) screening of human retinal pigment epithelial (RPE) cells identified TXNRD1 isoforms 2, 3, or 5, the reductase of the TXN system, as an intracellular target of ELV-N34. TXNRD1 silencing confirmed that the ELV-N34 target was isoform 2 or 3. This …

Mutational Analysis Of The Nitrogenase Carbon Monoxide Protective Protein Cown Reveals That A Conserved C‑Terminal Glutamic Acid Residue Is Necessary For Its Activity, Dustin L. Willard, Joshuah J. Arellano, Mitch Underdahl, Terrence M. Lee, Avinash S. Ramaswamy, Gabriella Fumes, Agatha Kliman, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN’s protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work …

Association Of Chlamydia Trachomatis Burden With The Vaginal Microbiota, Bacterial Vaginosis, And Metronidazole Treatment, Caleb M. Ardizzone, Christopher M. Taylor, Evelyn Toh, Rebecca A. Lillis, Jacob H. Elnaggar, John W. Lammons, Patricia Dehon Mott, Emily L. Duffy, Li Shen, Alison J. Quayle

School of Graduate Studies Faculty Publications

Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is a common coinfection with Chlamydia trachomatis (Ct), and BV-associated bacteria (BVAB) and their products have been implicated in aiding Ct evade natural immunity. Here, we determined if a non-optimal vaginal microbiota was associated with a higher genital Ct burden and if metronidazole, a standard treatment for BV, would reduce Ct burden or aid in natural clearance of Ct infection. Cervicovaginal samples were collected from women at enrollment and, if testing positive for Ct infection, at a follow-up visit approximately one week later. Cervical Ct burden was assessed by inclusion forming …

Structural Analysis And Activity Correlation Of Amphiphilic Cyclic Antimicrobial Peptides Derived From The [W4R4] Scaffold, Shaima Ahmed El-Mowafi, Anastasia G. Konshina, Eman H. M. Mohammed, Nikolay A. Krylov, Roman G. Efremov, Keykavous Parang

Pharmacy Faculty Articles and Research

In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, [W₄R₄], incorporating an extra aromatic hydrophobic residue (W), a positively charged residue (R), or the unique 2,5-diketopiperazine (DKP). This study systematically explored the structure–activity relationships (SARs) of a series of cyclic peptides derived from the [W₄R₄] scaffold, …

Analyzing Functional Interactions Of Designed Peptides By Nmr Spectroscopy, Wonsuk Choi

Pharmaceutical Sciences (MS) Theses

The development of small peptide-based therapeutics can be accelerated by the knowledge of relationships between the peptide structure and its functional interactions. Here, we report the analysis of two groups of synthetic peptides designed for two applications – broad bactericidal action and inhibition of protein-protein interactions in human cells. Novel amphiphilic peptides designed for antibacterial application incorporated arginine as cationic amino acids and non-natural amino acids that have aromatic side chains with similar hydrophobic properties as tryptophan. The interaction of lead cyclic peptides and their linear analogs with a phospholipid bilayer mimicking a bacterial membrane was studied using nuclear magnetic …

Environmental Exposures And Aging., Daniel Chris Gomes

Electronic Theses and Dissertations

In recent years, research into air pollution has shown that exposure to certain components in air pollution, primarily PM2.5 can accelerate biological aging and thereby lead to increased susceptibility to multiple diseases. We hypothesize that prolonged exposure to air pollutants can result in premature aging leading to extensive tissue dysfunction and susceptibility to diseases. To examine this, we exposed mice to PM2.5 for 9, 15, and 21 days, then measured the telomere lengths, cellular senescence, and histone methylation patterns of multiple cell types. We found consistently increased telomere attrition, cellular senescence and advanced age-consistent histone methylation patterns in groups exposed …

Incidence Of Rapidly Progressive Osteoarthritis Following Intra-Articular Hip Corticosteroid Injection: A Systematic Review And Meta-Analysis, Franco M. Sabatini, Anna Cohen-Rosenblum, Travis B. Eason, Charles P. Hannon, Samuel D. Mounce, Chad A. Krueger, F Winston Gwathmey, Stephen T. Duncan, David C. Landy

School of Medicine Faculty Publications

BACKGROUND: The American Academy of Orthopedic Surgery recommends intra-articular corticosteroid injections (CSIs) for managing hip osteoarthritis (OA) based on short-term, prospective studies. Recent retrospective studies have raised concerns that CSIs may lead to rapidly progressive OA (RPOA). We sought to systematically review the literature of CSIs for hip OA to estimate the incidence of RPOA. METHODS: MEDLINE, Embase, and Cochrane Library were searched to identify original research of hip OA patients receiving CSIs. Overall, 27 articles involving 5831 patients published from 1988 to 2022 were included. Study design, patient characteristics, CSI details, follow-up, and cases of RPOA were recorded. Studies …

The Evolving Role Of Vericiguat In Patients With Chronic Heart Failure, Ross M. Dies, Corrie N. Jackson, Chelsi J. Flanagan, Evan S. Sinnathamby, Noah J. Spillers, Pooja Potharaju, Naina Singh, Giustino Varrassi, Shahab Ahmadzadeh, Sahar Shekoohi, Alan D. Kaye

School of Medicine Faculty Publications

Heart failure (HF) is a chronic and progressive clinical disorder characterized by an inability to pump sufficient blood to meet metabolic demands. It poses a substantial global healthcare burden, leading to high morbidity, mortality, and economic impact. Current treatments for HF include lifestyle modifications, guideline-directed medical therapies (GDMT), and device interventions, but the need for novel therapeutic approaches remains significant. The introduction of vericiguat, a soluble guanylate cyclase stimulator, has shown promise in improving outcomes for heart failure patients. Vericiguat addresses the underlying pathophysiological mechanisms of heart failure by augmenting the cyclic guanosine monophosphate (cGMP) pathway, leading to enhanced cardiac …

November / December 2023, Randy Curry, Cindy Brooks

RURAL ROCKS

This is the November & December 2023 issue of Rural Rocks from the SWOSU College of Pharmacy.

Quality Assessment Of Hydroquinone, Mercury, And Arsenic In Skin-Lightening Cosmetics Marketed In Ilorin, Nigeria, Olasunkanmi David Bamidele, Blessing A. Kayode, Oluwasegun I. Eniayewu, Adebanjo J. Adegbola, Raphael S. Olatoye, Ngaitad S. Njinga, Sa’Ad T. Abdullahi, Moji T. Bakare-Odunola

Research outputs 2022 to 2026

Hydroquinone, Mercury (Hg), and Arsenic (As) are hazardous to health upon long-term exposure. Hydroquinone, Hg, and As were analysed in skin-lightening cosmetics randomly purchased from different cosmetic outlets within the Ilorin metropolis, Nigeria. The amount of hydroquinone in the samples was determined using a UV-spectrophotometry method at 290 nm. Hg and As were quantified using atomic absorption spectrophotometry (AAS). UV-spectrophotometry method validation showed excellent linearity (r2 = 0.9993), with limits of detection (0.75 g/mL), limits of quantification (2.28 g/mL), relative standard deviation (0.01–0.35%), and recovery (95.85–103.56%) in the concentration range of 5–50 g/mL. Similarly, r2, LOD, and LOQ for Hg …

Design Of An Fgf-1-Fgf-2 Heterodimer Variant With Enhanced Stability And Cell Proliferation Activity, Nicholas Alan Pohlman

Chemistry & Biochemistry Undergraduate Honors Theses

The FGF-1 subfamily, composed of FGF-1 and FGF-2, assists in broad health-related processes such as cell proliferation and angiogenesis respectively.^1,2 The subfamily shows promising signs as a therapeutic, however, the inherent thermal instability leads to a low half-life in vivo.³ To assist in improving the stability, FGF-1 and FGF-2 were connected via a 12-residue glycine linker ultimately producing a heterodimer. This heterodimer was further examined to discover its novel properties. Inspiration for this project was drawn from previous research which performed five mutations on FGF-1 ultimately improving stability in the protein complex. In addition to these five …

Circulating Pre-Treatment T-Cell Receptor Repertoire As A Predictive Biomarker In Advanced Or Metastatic Non-Small-Cell Lung Cancer Patients Treated With Pembrolizumab Alone Or In Combination With Chemotherapy, A. Abed, Aaron B. Beasley, Anna L. Reid, N. Law, L. Calapre, M. Millward, Johnny Lo, Elin S. Gray

Research outputs 2022 to 2026

Background: The circulating T-cell receptor (TCR) repertoire is a dynamic representation of overall immune responses in an individual. Materials and methods: We prospectively collected baseline blood from patients treated with first-line pembrolizumab monotherapy or in combination with chemotherapy. TCR repertoire metrics were correlated with clinical benefit rate (CBR), progression-free survival (PFS), overall survival (OS) and immune-related adverse events (irAEs). We built a logistic regression classifier by fitting all four TCR- repertoire metrics to the immune checkpoint inhibitor (ICI) CBR data. In the subsequent receiver operating characteristic (ROC) analysis of the resulting logistic regression model probabilities, the best cut-off value was …

Improving Estimation Of Coronary Artery Disease Risk Using Haptoglobin Genotyping, Emily Kate Mewborn

Theses and Dissertations (ETD)

Atherosclerotic cardiovascular disease (ASCVD) continues to be the leading cause of death worldwide. While several risk factors contributing to disease progression are well-known, pitfalls and limitations exist for estimating if or when an individual will develop the disease. Coronary artery disease (CAD), a subtype of ASCVD, causes myocardial infarction, contributing to significant morbidity and mortality. Current ASCVD risk estimator calculators lack comprehensiveness and do not include genetic or social determinants of health information, which are known to affect ASCVD risk.

Haptoglobin (Hp) genotype also influences CAD risk. Hp is a protein that binds free hemoglobin released from physiologic or pathologic …

How Carvedilol Does Not Activate Β2-Adrenoceptors, Robert J. Lefkowitz, Howard A. Rockman, Paul J. Shim, Samuel Liu, Seungkirl Ahn, Biswaranjan Pani, Sudarshan Rajagopal, Sudha K. Shenoy, Michel Bouvier, Jeffrey L. Benovic, Stephen B. Liggett, Robert R. Ruffolo, Michael R. Bristow, Milton Packer

Department of Biochemistry and Molecular Biology Faculty Papers

No abstract provided.

Dietary Analysis For Hashimoto’S Thyroiditis: An Integrative Review, Evan Thompson, Alison Hultquist

Master of Science in Nursing Final Projects

Abstract

Hashimoto’s Thyroiditis (HT) is the leading cause of primary hypothyroidism in the United States. In HT, there is an infiltration by lymphocytes which leads to the production of autoantibodies against the thyroid gland. Throughout this integrative review, the aim was to evaluate the effectiveness of micronutrient supplementation and dietary management as adjunct treatments in HT. The purpose was to assist primary care providers in the development of a more holistic plan of care. Literature published within the past seven years was gathered and reviewed from PubMed, CINAHL, and Cochrane Library. Findings indicate that many patients with HT may benefit …

Effectiveness Of A Bivalent Mrna Vaccine Dose Against Symptomatic Sars-Cov-2 Infection Among U.S. Healthcare Personnel, September 2022–May 2023, Ian D. Plumb, Melissa Briggs Hagen, Ryan Wiegand, Ghinwa Dumyati, Christopher Myers, Karisa K. Harland, Anusha Krishnadasan, Jade James Gist, Glen Abedi, Katherine E. Fleming-Dutra, Nora Chea, Jane E. Lee, Melissa Kellogg, Alexandra Edmundson, Amber Britton, Lucy E. Wilson, Sara A. Lovett, Valerie Ocampo, Tiffanie M. Markus, Howard A. Smithline, Peter C. Hou, Lilly C. Lee, William Mower, Fernand Rwamwejo, Mark T. Steele, Stephen C. Lim, Walter A. Schrading, Brian Chinnock

School of Medicine Faculty Publications

Background: Bivalent mRNA vaccines were recommended since September 2022. However, coverage with a recent vaccine dose has been limited, and there are few robust estimates of bivalent VE against symptomatic SARS-CoV-2 infection (COVID-19). We estimated VE of a bivalent mRNA vaccine dose against COVID-19 among eligible U.S. healthcare personnel who had previously received monovalent mRNA vaccine doses. Methods: We conducted a case-control study in 22 U.S. states, and enrolled healthcare personnel with COVID-19 (case-participants) or without COVID-19 (control-participants) during September 2022–May 2023. Participants were considered eligible for a bivalent mRNA dose if they had received 2–4 monovalent (ancestral-strain) mRNA vaccine …

Prefrontal Cortex Glutamatergic Adaptations In A Mouse Model Of Alcohol Use Disorder, Mahum T. Siddiqi, Dhruba Podder, Amanda R. Pahng, Alexandria C. Athanason, Tali Nadav, Chelsea Cates-Gatto, Max Kreifeldt, Candice Contet, Amanda J. Roberts, Scott Edwards, Marisa Roberto, Florence P. Varodayan

School of Graduate Studies Faculty Publications

Alcohol use disorder (AUD) produces cognitive deficits, indicating a shift in prefrontal cortex (PFC) function. PFC glutamate neurotransmission is mostly mediated by α-amino-3‑hydroxy-5-methyl-4-isoxazolepropionic acid-type ionotropic receptors (AMPARs); however preclinical studies have mostly focused on other receptor subtypes. Here we examined the impact of early withdrawal from chronic ethanol on AMPAR function in the mouse medial PFC (mPFC). Dependent male C57BL/6J mice were generated using the chronic intermittent ethanol vapor-two bottle choice (CIE-2BC) paradigm. Non-dependent mice had access to water and ethanol bottles but did not receive ethanol vapor. Naïve mice had no ethanol exposure. We used patch-clamp electrophysiology to measure …

A Novel Function Of Protein S In Clot Retraction, Narender Kumar, Alaina Guilbeau, V. Pilli, Rinku Majumder

School of Medicine Faculty Publications

ISTH 2023 Congress, June 24 - 28, 2023, Montreal, Canada

Antiphosphatidylserine/Prothrombin Antibodies In Childhood Sle Are Associated With Lupus Anticoagulant Positivity, S. Chugh, R. Pilania, A. Kler, C. Hans, Narender Kumar, S. Singh, J. Ahluwalia

School of Medicine Faculty Publications

ISTH 2023 Congress, June 24 - 28, 2023, Montreal, Canada

Regulation Of Protein S Gene Expression By Hypoxia Inducible Factor 1 Α And Estrogen Receptor, Mohammad Mohammad, V. Pilli, M. Kumar, Alaina Guilbeau, Narender Kumar, Rinku Majumder

School of Medicine Faculty Publications

ISTH 2023 Congress June 24-28, 2023, Montreal, Canada

Long-Acting Cabotegravir And The Emergence Of Drug-Resistant Hiv, Katharine Gurski

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Application Of Electrosprayed Minocycline-Loaded Plga Microparticles For The Treatment Of Glioblastoma, Marco Antonio Arriaga, Juan A. Amieva, Jaqueline Quintanilla, Angela C. Jimenez, Julio Ledezma, Silverio A. Lopez, Karen S. Martirosyan, Sue Anne Chew

Health & Biomedical Sciences Faculty Publications

The survival of patients with glioblastoma multiforme (GBM), the most common and invasive form of malignant brain tumors, remains poor despite advances in current treatment methods including surgery, radiotherapy, and chemotherapy. Minocycline is a semi-synthetic tetracycline derivative that has been widely used as an antibiotic and more recently, it has been utilized as an antiangiogenic factor to inhibit tumorigenesis. The objective of this study was to investigate the utilization of electrospraying process to fabricate minocycline-loaded poly(lactic-co-glycolic acid) (PLGA) microparticles with high drug loading and loading efficiency and to evaluate their ability to induce cell toxicity in human glioblastoma (i.e., U87-MG) …

Proton Pump Inhibitor Use And Adverse Effects In South Atlantic Hospitals, Nicholas D'Angelo, Ramyar Sigarchy, Anthony Esswein, Sidra Asrar

HCA Healthcare Journal of Medicine

Background

Proton pump inhibitors (PPI) have transformed the management of acid-related gastrointestinal disorders, becoming one of the top-selling medications in the United States. There is no doubt that PPIs have a significant therapeutic impact on patients with gastroesophageal reflux disease and gastrointestinal bleeding. However, evidence is mounting that PPIs are overprescribed, leading to more patients possibly experiencing adverse effects. There is a great deal of ongoing debate surrounding the significance and impact of these adverse effects.

Methods

We conducted a study in 9 HCA hospitals in the southeastern United States to determine the number of patients who started on PPIs …

Molecular Docking And Dynamics Identify Potential Drugs To Be Repurposed As Sars-Cov-2 Inhibitors, Mohammed Muzaffar-Ur-Rehman, Chougule K. Suryakant, Ala Chandu, Banoth K. Kumar, Renuka P. Joshi, Snehal R. Jadav, Murugesan Sankaranarayanan, Seshadri S. Vasan

Research outputs 2022 to 2026

The novel coronavirus disease 19 (COVID-19) has resulted in an estimated 20 million excess deaths and the recent resurgence of COVID-19 in China is predicted to result in up to 1 million deaths over the next few months. With vaccines being ineffective in the case of immunocompromised patients, it is important to continue our quest for safe, effective and affordable drugs that will be available to all countries. Drug repurposing is one of the strategies being explored in this context. Recently, out of the 7817 drugs approved worldwide, 214 candidates were systematically down-selected using a combination of 11 filters including …

Determining The Ideal Concentrations Of Ethanol And Propylene Glycol In Ethosomes For Transdermal Delivery Of Vitamin D3, Rebecca Conner

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Vitamin D₃ is an important chemical in the human body, however, many Americans have low levels of this vitamin. There are plenty of oral supplementations for Vitamin D₃ deficiency, but those of older age and busy schedules may struggle to meet the minimum requirement. A recently developed ethosomal transmembrane delivery system (Touitou, 2000), similar to liposomes but also containing ethanol, allows users to apply a gel dermally and have the desired drug or active ingredient reach the bloodstream faster. However, there is considerable variation in the concentration of ethanol and permeation enhancers used. Using an affordable method to …

Ca2+-Regulated Expression Of High Affinity Methylaminoisobutryic Acid Transport In Hippocampal Neurons Inhibited By Riluzole And Novel Neuroprotective Aminothiazoles, Jeffrey D. Erickson, Thomas Kyllo, Heike Wulff

School of Medicine Faculty Publications

High affinity methylaminoisobutyric acid(MeAIB)/glutamine(Gln) transport activity regulated by neuronal firing occurs at the plasma membrane in mature rat hippocampal neuron-enriched cultures. Spontaneous Ca2+-regulated transport activity was similarly inhibited by riluzole, a benzothiazole anticonvulsant agent, and by novel naphthalenyl substituted aminothiazole derivatives such as SKA-378. Here, we report that spontaneous transport activity is stimulated by 4-aminopyridine (4-AP) and that phorbol-myristate acetate (PMA) increases high K+ stimulated transport activity that is inhibited by staurosporine. 4-AP-stimulated spontaneous and PMA-stimulated high K+-induced transport is not present at 7 days in vitro (DIV) and is maximal by DIV∼21. The relative affinity for MeAIB is similar …

The Inherited Kras-Variant As A Biomarker Of Cetuximab Response In Nsclc, Joanne Weidhaas, Chen Hu, Ritsuko Komaki, Gregory Masters, George Blumenschein, Joe Chang, Bo Lu, Adam Dicker, Jeffrey Bogart, Yolanda Garces, Samir Narayan, Clifford Robinson, Vivek Kavadi, Joel S Greenberger, Christopher Koprowski, James Welsh, Elizabeth Gore, Robert Macrae, Rebecca Paulus, Jeffrey Bradley

Department of Radiation Oncology Faculty Papers

PURPOSE: RTOG 0617 was a phase III randomized trial for patients with unresectable stage IIIA/IIIB non-small cell lung cancer comparing standard-dose (60 Gy) versus high-dose (74 Gy) radiotherapy and chemotherapy, plus or minus cetuximab. Although the study was negative, based on prior evidence that patients with the KRAS-variant, an inherited germline mutation, benefit from cetuximab, we evaluated KRAS-variant patients in RTOG 0617.

EXPERIMENTAL DESIGN: From RTOG 0617, 328 of 496 (66%) of patients were included in this analysis. For time-to-event outcomes, stratified log-rank tests and multivariable Cox regression models were used. For binary outcomes, Cochran-Mantel-Haenzel tests and multivariable logistic regression …

Comparative Analysis Of Conformational Dynamics And Systematic Characterization Of Cryptic Pockets In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb.1 Spike Complexes With The Ace2 Host Receptor: Confluence Of Binding And Structural Plasticity In Mediating Networks Of Conserved Allosteric Sites, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes …