Welcome to the

GlyCORE Computational Chemistry and Bioinformatics Research CORE (CCBRC)

of the

Glycoscience Center of Research Excellence (GlyCORE)

at the

University of Mississippi

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Dr. Doerksen directs the NIH-funded Computational Chemistry and Bioinformatics Research Core (CCBRC), which provides computations, resources and training of many kinds to support research on multiple glycoscience topics, including for modeling of glycoprotein structure, dynamics, and interactions; modeling of carbohydrates and natural-product sugar-containing molecules; and lectin-carbohydrate interactions.

Recent Workshop:

CCBRC Workshop: Protein Structure Prediction and Glycosylation

Thursday, November 10, 2022, 9:00 a.m. – 12:00 p.m., 106E, J. D. Williams Library, University of Mississippi

With hands-on software training in Modeller, AlphaFold, and Charmm-GUI. Register here.

GlyCORE Workshops and Training Seminars

Example of Prior Workshop:

Hands-on Computational Glycoscience Workshop, January 28-29, 2021

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Dr. Mohamed Jahan joined the CCBRC as a postdoctoral fellow, effective 1/2023!

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Abby Haskew joined the CCBRC as an undergraduate research student, effective 5/2023!

Dr. Sushil K. Mishra, Research Scientist, has now joined Dr. Doerksen’s research group and CCBRC, as CORE Manager, effective October 2020!

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Priyanka Samanta, PhD student, has now joined Dr. Doerksen’s research group and CCBRC, effective August 2020!

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GlyCORE CCBRC is funded by US National Institute of General Medical Sciences of the National Institutes of Health (NIH) under Award Number P20GM130460 (5/15/2020-3/31/2025). The research is solely the responsibility of the researchers and does not necessarily represent the official views of the NIH.

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Founded in 1848, the University of Mississippi (UM) is included in the elite group of R-1: Doctoral Universities – Highest Research Activity by the Carnegie Classification. UM is consistently named by The Chronicle of Higher Education as a “Great College to Work for,” and is located in Oxford, MS, which is ranked one of the “Top 10 Best College Towns,” in the rolling hills of north Mississippi 70 miles south of Memphis, Tennessee. Oxford has small town charm and has been featured as a literary and arts destination in such publications as The New York Times and GQ.

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Are you interested in computations relevant to glycoscience?

• Collaboration?

• Contract research done for you?

• Training for you and/or your research team members?

If so, we can help you. Please contact the Core Director, Prof. Robert Doerksen (www.robertjdoerksen.com).

Submit:

1. Name of the investigator

2. Name of the group leader (if different)

3. Institution or company name

4. Contact information

5. Nature of the project

What kinds of calculations are covered?

• Structures and properties of small molecules containing sugar moieties

• Structures and properties of glycoconjugates such as glycoproteins

• Protein-ligand interactions in which either the protein or ligand or both contain glyco groups

• Bioinformatics analysis of big data such as the outputs of mass spectrometry of glycoconjugate mixtures

• Other bioinformatics, such as for pathway analysis of glycosylation

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What does “CORE” mean? It stands for “Center of Research Excellence”.

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What are some relevant publications from the Doerksen research group?

• R Alkhodier; SK Mishra; RJ Doerksen; DA Colby “Comparison of conformational analyses of naturally occurring flavonoid-O-glycosides with unnatural flavonoid-CF2-glycosides using molecular modeling,” Journal of Chemical Information & Modeling 63, 375-386 (2023). doi: 10.1021/acs.jcim.2c01147 PMID: 36512328
• SB Kim; M Farrag; SK Mishra; SK Misra; JS Sharp; RJ Doerksen; VH Pomin “Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis,” Carbohydrate Polymers 301A, 120316 (2023). doi: 10.1016/j.carbpol.2022.120316 PMID: 36436858
• OT Shofolawe-Bakare; JU de Mel; SK Mishra; MA Hossain; CM Hamadani; MC Pride; GS Dasanayake; WA Monroe; EW Roth; EEL Tanner; RJ Doerksen; AE Smith; TA Werfel “ROS-responsive glycopolymeric nanoparticles for enhanced drug delivery to macrophages,” Macromolecular Bioscience 22, 202200281 (2022). doi: 10.1002/mabi.202200281 PMID: 36125638
• M Nagae; T Hirata; H Tateno; SK Mishra; N Manbe; N Osada; Y Tokoro; Y Yamaguchi; RJ Doerksen; T Shimizu; Y Kizuka “Discovery of a lectin domain that regulates enzyme activity in mouse N-acetylglucosaminyltransferase-IVa (MGAT4A),” Communications Biology 5, 695 (2022). doi: 10.1038/s42003-022-03661-w PMID: 35854001
• SB Kim; M Zoepfl; P Samanta; F Zhang; K Xia; R Thara; RJ Linhardt; RJ Doerksen; MA McVoy; VH Pomin “Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties,” Journal of Biological Chemistry 101856 (accepted 3/22/2022). doi: 10.1016/j.jbc.2022.101856
• AM Vibhute; H-N Tanaka; SK Mishra; M Nagae; C Yonekawa; H Korekane; RJ Doerksen; H Ando; Y Kizuka “Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors,” accepted to BBA General Subjects 1866(6): 130118 (3/4/2022). doi: 10.1016/j.bbagen.2022.130118 PMID: 35248671.
• R Dwivedi; P Samanta; P Sharma; F Zhang; SK Mishra; P Kucheryavy; SB Kim; AO Aderibigbe; RJ Linhardt; R Tandon; RJ Doerksen; VH Pomin “Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection,” Journal of Biological Chemistry 297, 101207 (2021). doi: 10.1016/j.jbc.2021.101207 PMID: 34537241
• VK Shankar; A Police; P Pandey; ZG Cuny; MA Repka; RJ Doerksen; SN Murthy “Optimization of sulfobutyl-ether-β-cyclodextrin levels in oral formulations to enhance progesterone bioavailability,” International Journal of Pharmaceutics 596, 120212 (2021). doi: 10.1016/j.ijpharm.2021.120212
• FF Bezerra; WP Vignovich; AO Aderibigbe; H Liu; J Sharp; RJ Doerksen; VH Pomin “Conformational properties of L-fucose and the tetrasaccharide building block of the sulfated L-fucan from Lytechinus variegatus,” Journal of Structural Biology 209, 107407 (2020). doi: 10.1016/j.jsb.2019.107407 PMID: 31698075

• Y Zou; X Wang; J Sims; B Wang; P Pandey; CL Welsh; RP Stone; MA Avery; RJ Doerksen; D Ferreira; C Anklin; FA Valeriote; M Kelly; MT Hamann “Computationally-assisted discovery and assignment of a highly strained and PANC-1 selective alkaloid from Alaska’s deep ocean,” Journal of the American Chemical Society 141, 4338-4344 (2019). doi: 10.1021/jacs.8b11403 PMID: 30758203

• LG Malak; MA Ibrahim; AM Moharram; P Pandey; B Tekwani; RJ Doerksen; D Ferreira; SA Ross “Antileishmanial Carbasugars from Geosmithia langdonii,” Journal of Natural Products 81, 2222-2227 (2018). doi: 10.1021/acs.jnatprod.8b00473 PMID: 30298736
• NN Mohammed; P Pandey; KM Elokely; HL Liu; RJ Doerksen; MA Repka “Clotrimazole-cyclodextrin based approach for the management and treatment of Candidiasis. A formulation and chemistry based evaluation,” Pharmaceutical Development and Technology, 21, 619-629 (2016). doi: 10.3109/10837450.2015.1041041 PMID: 25923135
• MM Ghoneim; KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; M Radwan; RJ Doeksen; SJ Cutler; SA Ross “Asphodosides A-E, anti-MRSA metabolites from Asphodelus microcarpus,” Phytochemistry, 105, 79-84 (2014). doi: 10.1016/j.phytochem.2014.06.011         
• MM Ghoneim, KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; SJ Cutler; RJ Doerksen; SA Ross “Isolation and characterization of new secondary metabolites from Asphodelus microcarpus,” Medicinal Chemistry Research, 23, 3510-3515 (2014). doi: 10.1007/s00044-014-0928-x
• KM Elokely; RJ Doerksen “Docking challenge: Protein sampling and molecular docking performance,” Journal of Chemical Information & Modeling, 53, 1934–1945 (2013). doi: 10.1021/ci400040d PMID: 23530568 Featured on the cover of Issue 11, November 2013. Cited >107 times.