GlyCORE Publications

04/01/2023 - 03/31/2024 

Samanta P, Mishra SK, Pomin VH, Doerksen RJ. Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein. Molecules. 2023; 28(17):6413. https://doi.org/10.3390/molecules28176413. Published September 3, 2023.

Samanta P, Doerksen RJ. Identifying FmlH lectin-binding small molecules for the prevention of Escherichia coli-induced urinary tract infections using hybrid fragment-based design and molecular docking, Computers in Biology and Medicine, Volume 163, 2023, 107072, ISSN 0010-4825. https://doi.org/10.1016/j.compbiomed.2023.107072. Published September 2023.

Ahearne A, Phillips KE, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism. Front Microbiol. 2023 Aug 3;14:1227206. doi: 10.3389/fmicb.2023.1227206. PMID: 37601375; PMCID: PMC10435759.

Islam, B.; Colby, D. A. Transient Formation of Hemiketals from Pentafluoro-gem-diols in the Presence of Alcohols. J. Fluorine Chem. 2023, 270, 110162. DOI: 10.1016/j.jfluchem.2023.110162 Published August 2023.

Dwivedi R, Farrag M, Sharma P, Shi D, Shami AA, Misra SK, Ray P, Shukla J, Zhang F, Linhardt RJ, Sharp JS, Tandon R, Pomin VH. The Sea Cucumber Thyonella gemmata Contains a Low Anticoagulant Sulfated Fucan with High Anti-SARS-CoV-2 Actions against Wild-Type and Delta Variants. J Nat Prod. 2023 Jun 23;86(6):1463-1475. doi: 10.1021/acs.jnatprod.3c00151. Epub 2023 Jun 12. PMID: 37306476; PMCID: PMC10401483.

Antim K. Maurya, Poonam Sharma, Priyanka Samanta, Anter A. Shami, Sandeep K. Misra, Fuming Zhang, Reena Thara, Deepak Kumar, Deling Shi, Robert J. Linhardt, Joshua S. Sharp, Robert J. Doerksen, Ritesh Tandon, Vitor H. Pomin, Structure, anti-SARS-CoV-2, and anticoagulant effects of two sulfated galactans from the red alga Botryocladia occidentalis, International Journal of Biological Macromolecules, 2023, 124168, ISSN 0141-8130, https://doi.org/10.1016/j.ijbiomac.2023.124168. Published May 31, 2023.

Farrag M, Dwivedi R, Sharma P, Kumar D, Tandon R, Pomin VH. Structural requirements of Holothuria floridana fucosylated chondroitin sulfate oligosaccharides in anti-SARS-CoV-2 and anticoagulant activities. PLoS One. 2023 May 11;18(5):e0285539. doi: 10.1371/journal.pone.0285539. PMID: 37167245; PMCID: PMC10174540. Published May 11, 2023.

He P, Shi D, Li Y, Xia K, Kim SB, Dwivedi R, Farrag M, Pomin VH, Linhardt RJ, Dordick JS, Zhang F. SPR Sensor-Based Analysis of the Inhibition of Marine Sulfated Glycans on Interactions between Monkeypox Virus Proteins and Glycosaminoglycans. Mar Drugs. 2023 Apr 25;21(5):264. doi: 10.3390/md21050264. PMID: 37233458; PMCID: PMC10222398.

GlyCORE Publications

04/01/2022 - 03/31/2023 

Sharma P, Dwivedi R, Ray P, Shukla J, Pomin VH, Tandon R. Inhibition of Cytomegalovirus by Pentacta pygmaea Fucosylated Chondroitin Sulfate Depends on Its Molecular Weight. Viruses. 2023; 15(4):859. https://doi.org/10.3390/v15040859 Published March 28, 2023.

Zoepfl, M., Dwivedi, R., Kim, S.B. et al. Antiviral activity of marine sulfated glycans against pathogenic human coronaviruses. Sci Rep 13, 4804 (2023). https://doi.org/10.1038/s41598-023-31722-5 Published March 23, 2023.

Seon Beom Kim, Marwa Farrag, Sushil K. Mishra, Sandeep K. Misra, Joshua S. Sharp, Robert J. Doerksen, Vitor H. Pomin, Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis, Carbohydrate Polymers, Volume 301, Part A, 2023, 120316, ISSN 0144-8617, https://doi.org/10.1016/j.carbpol.2022.120316  Published February 1, 2023.

Alkhodier RA, Mishra SK, Doerksen RJ, Colby DA. Comparison of Conformational Analyses of Naturally Occurring Flavonoid-O-Glycosides with Unnatural Flavonoid-CF₂-Glycosides Using Molecular Modeling. J Chem Inf Model. 2023 Jan 9;63(1):375-386. doi: 10.1021/acs.jcim.2c01147. Epub 2022 Dec 13. PMID: 36512328.

Cheng Z, Misra SK, Shami A, Sharp JS. Structural Analysis of Phosphorylation Proteoforms in a Dynamic Heterogeneous System Using Flash Oxidation Coupled In-Line with Ion Exchange Chromatography. Anal Chem. 2022 Dec 27;94(51):18017-18024. doi: 10.1021/acs.analchem.2c04365. Epub 2022 Dec 13. PMID: 36512753; PMCID: PMC9912381.

Ahmed, H.A., Ticar, B.F., Black, I., Mahdi, F., Shami, A.A., Misra, S.K., Heiss, C., Paris, J.J., Sharp, J.S., Azadi, P., Pomin, V.H. Structural characterization and biological activity of an α-glucan from the mollusk Marcia hiantina (Lamarck, 1818). Glycoconj J (2022). https://doi.org/10.1007/s10719-022-10092-6 (Published December 1, 2022)

Bajracharya A, Xi J, Grace KF, Bayer EE, Grant CA, Clutton CH, Baerson SR, Agarwal AK, Qiu Y. PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the Mediator subunit MED14. Plant Physiol. 2022 Nov 28;190(4):2706-2721. doi: 10.1093/plphys/kiac412. PMID: 36063057; PMCID: PMC9706435.

De Mel J, Hossain M, Shofolawe-Bakare O, Mohammad SA, Rasmussen E, Milloy K, Shields M, Roth EW, Arora K, Cueto R, Tang SC, Wilson JT, Smith AE, Werfel TA. Dual-Responsive Glycopolymers for Intracellular Codelivery of Antigen and Lipophilic Adjuvants. Mol Pharm. 2022 Dec 5;19(12):4705-4716. doi: 10.1021/acs.molpharmaceut.2c00750. Epub 2022 Nov 14. PMID: 36374992.

Phillips KE, Akbar S, Stevens DC. Concepts and conjectures concerning predatory performance of myxobacteria. Frontiers in Microbiology. 2022 Sep 29 doi.org/10.3389/fmicb.2022.1031346

Rohini Dwivedi, Poonam Sharma, Friederike Eilts, Fuming Zhang, Robert J Linhardt, Ritesh Tandon, Vitor H Pomin, Anti-SARS-CoV-2 and anticoagulant properties of Pentacta pygmaea fucosylated chondroitin sulfate depend on high molecular weight structures, Glycobiology, 2022;, cwac063, doi.org/10.1093/glycob/cwac063

Shofolawe-Bakare OT, de Mel JU, Mishra SK, Hossain M, Hamadani CM, Pride MC, Dasanayake GS, Monroe W, Roth EW, Tanner EEL, Doerksen RJ, Smith AE, Werfel TA. ROS-Responsive Glycopolymeric Nanoparticles for Enhanced Drug Delivery to Macrophages. Macromol Biosci. 2022 Dec;22(12):e2200281. doi: 10.1002/mabi.202200281. Epub 2022 Sep 28. PMID: 36125638. https://doi.org/10.1002/mabi.202200281

Zhang W, Jin W, Pomin VH, Zhang F and Linhardt RJ (2022) Interactions of marine sulfated glycans with antithrombin and platelet factor 4. Front. Mol. Biosci. 9:954752. doi: 10.3389/fmolb.2022.954752. Published 19 September 2022.

Nagae M, Hirata T, Tateno H, Mishra SK, Manabe N, Osada N, Tokoro Y, Yamaguchi Y, Doerksen RJ, Shimizu T, Kizuka Y. Discovery of a lectin domain that regulates enzyme activity in mouse N-acetylglucosaminyltransferase-IVa (MGAT4A). Commun Biol. 2022 Jul 19;5(1):695. doi: 10.1038/s42003-022-03661-w. PMID: 35854001; PMCID: PMC9296478.

Fortenberry A, Mohammad SA, Werfel TA, Smith AE. Comparative Investigation of the Hydrolysis of Charge-Shifting Polymers Derived from an Azlactone-Based Polymer. Macromol Rapid Commun. 2022 Jul 12:e2200420. doi: 10.1002/marc.202200420. Epub ahead of print. PMID: 35820157.

Dwivedi R, Sharma P, Farrag M, Kim SB, Fassero LA, Tandon R, Pomin VH. Inhibition of SARS-CoV-2 wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) strains by marine Sulfated Glycans. Glycobiology. 2022 Jul 5:cwac042. doi: 10.1093/glycob/cwac042. Epub ahead of print. PMID: 35788318. (Published July 5, 2022)

Vibhute AM, Tanaka HN, Mishra SK, Osuka RF, Nagae M, Yonekawa C, Korekane H, Doerksen RJ, Ando H, Kizuka Y. Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors. Biochim Biophys Acta Gen Subj. 2022 Jun;1866(6):130118. doi: 10.1016/j.bbagen.2022.130118. Epub 2022 Mar 4. PMID: 35248671. https://doi.org/10.1016/j.bbagen.2022.130118. (Published June 2022)

Jakka D, Matadh AV, Shankar VK, Shivakumar HN, Narasimha Murthy S. Polymer Coated Polymeric (PCP) Microneedles for Controlled Delivery of Drugs (Dermal and Intravitreal). J Pharm Sci. 2022 Oct;111(10):2867-2878. doi: 10.1016/j.xphs.2022.05.023. Epub 2022 May 31. PMID: 35662543.

Khaje NA, Eletsky A, Biehn SE, Mobley CK, Rogals MJ, Kim Y, Mishra SK, Doerksen RJ, Lindert S, Prestegard JH, Sharp JS. Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol. 2022 May 12;5(1):452. doi: 10.1038/s42003-022-03411-y. PMID: 35551273; PMCID: PMC9098640.

Khatri HR, Han C, Alkhodier RA, Adam AT, Islam B, Colby DA. Generation of formaldehyde and formaldehyde-d₂ for hydroxymethylations and hydroxydeuteromethylations of difluoroenolates and difluorobenzyl carbanions. Chem Commun (Camb). 2022 May 3;58(36):5490-5493. doi: 10.1039/d2cc01518h. PMID: 35416212; PMCID: PMC9205602.  (Published April 13, 2022)

GlyCORE Publications

04/01/2021 - 03/31/2022 

Janke, Jonathan; Yu, Yanlei; Pomin, Vitor; Zhao, Jing; Wang, Chunyu; Linhardt, Robert; Garcia, Angel. Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. Journal of Chemical Theory and Computation (2022), doi: https://doi.org/10.1021/acs.jctc.1c00760 (Published Feb. 2, 2022)

Harris HM, Boyet KL Liu H, et al. Safety and Pharmacokinetics of Intranasally Administered Heparin. Pharmaceutical Research. 2022 Mar;39(3):541-551. doi: 10.1007/s11095-022-03191-4. PMID: 35237922; PMCID: PMC8890767.

Mitra S, Talukdar K, Prasad P, Misra SK, Khan S, Sharp JS, Jurss JW, Chakraborty S. Rational Design of a Cu Chelator That Mitigates Cu-Induced ROS Production by Amyloid Beta. Chembiochem. 2022 Feb 16;23(4):e202100485. doi: 10.1002/cbic.202100485. Epub 2021 Dec 30. PMID: 34878720; PMCID: PMC9040527.

Akbar S, Phillips KE, Misra SK, Sharp JS, Stevens DC. Differential response to prey quorum signals indicates predatory specialization of myxobacteria and ability to predate Pseudomonas aeruginosa. Environ Microbiol. 2022. Mar; 24(3):1263-1278. doi: 10.1111/1462-2920.15812. PubMed PMID: 34674390. (Epub Oct 21, 2021)

Dwivedi R, Samanta P, Sharma P, Zhang F, Mishra SK, Kucheryavy P, Kim SB, Aderibigbe AO, Linhardt RJ, Tandon R, Doerksen RJ, Pomin VH, Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection, Journal of Biological Chemistry (2021), doi: https://doi.org/10.1016/j.jbc.2021.101207 (Published Sept. 16, 2021)

Kawade H, Morise J, Mishra SK, Tsujioka S, Oka S, Kizuka Y. Tissue-Specific Regulation of HNK-1 Biosynthesis by Bisecting GlcNAc. Molecules. 2021 Aug 26;26(17):5176. doi: 10.3390/molecules26175176. PMID: 34500611; PMCID: PMC8434142.

Mitra S, Prakash D, Rajabimoghadam K, Wawrzak Z, Prasad P, Wu T, Misra SK, Sharp JS, Garcia-Bosch I, Chakraborty S. De Novo Design of a Self-Assembled Artificial Copper Peptide that Activates and Reduces Peroxide. ACS Catal. 2021 Aug 20;11(16):10267-10278. doi: 10.1021/acscatal.1c02132. Epub 2021 Aug 3. PMID: 36188417; PMCID: PMC9524465.

Pomin VH, Mahdi F, Jin W, Zhang F, Linhardt RJ, Paris JJ. Red Algal Sulfated Galactan Binds and Protects Neural Cells from HIV-1 gp120 and Tat. Pharmaceuticals. 2021; 14(8):714. https://doi.org/10.3390/ph14080714. (Published July 23, 2021)

Akbar, S., Stevens, D.C. Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator. Sci Rep 11, 16445 (2021). doi: https://doi.org/10.1038/s41598-021-96046-8 (Published Aug. 12, 2021)

Ahearne A, Albataineh H, Dowd SE, Stevens DC. Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. Microorganisms. 2021; 9(7):1376. https://doi.org/10.3390/microorganisms9071376. (Published June 24, 2021)

Sowaileh MF, Alshammari MD, Colby DA. Synthesis of Difluorinated Halohydrins by the Chemoselective Addition of Difluoroenolates to α-Haloketones. Organic Letters 2021 23 (13), 5098-5101. doi: 10.1021/acs.orglett.1c01636. (Published June 14, 2021)

Cheng Z, Mobley C, Misra SK, Gadepalli RS, Hammond RI, Brown LS, Rimoldi JM, Sharp JS. Self-Organized Amphiphiles Are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments. J Am Soc Mass Spectrom. 2021 May 5;32(5):1155-1161. doi: 10.1021/jasms.0c00457. Epub 2021 Apr 21. PMID: 33881849; PMCID: PMC8790760.

Adaikpoh BI, Dowd SE, Stevens DC. Draft Genome Sequence of Aneurinibacillus sp. Strain BA2021, Isolated as a Contaminant of a Laboratory-Cultivated Predatory Myxobacterium. Microbiol Resour Announc. 2021;10(17):e00243-21.  doi:10.1128/MRA.00243-21. (Published April 29, 2021)

Zoepfl M, Dwivedi R, Taylor MC, Pomin VH, McVoy MA. Antiviral activities of four sulfated marine glycans against adenovirus and human cytomegalovirus. Antiviral Res. 2021 Apr 14:105077. doi: 10.1016/j.antiviral.2021.105077. Epub ahead of print. PMID: 33864843. (Published April 14, 2021)

05/15/2020 - 03/31/2021

Tadi S, Misra SK, Sharp JS. Inline Liquid Chromatography-Fast Photochemical Oxidation of Proteins for Targeted Structural Analysis of Conformationally Heterogeneous Mixtures. Anal Chem. 2021 Feb 23;93(7):3510-3516. doi: 10.1021/acs.analchem.0c04872. Epub 2021 Feb 9. PMID: 33560821; PMCID: PMC7951798.

Alshammari MD, Kucheryavy PV, Ashpole NM, Colby DA. Synthesis, biological evaluation, and NMR studies of 3-fluorinated derivatives of 3',4',5'-trihydroxyflavone and 3',4',5'-trimethoxyflavone. Bioorg Med Chem Lett. 2021 Jan 15;32:127720. doi: 10.1016/j.bmcl.2020.127720. Epub 2020 Nov 28. PMID: 33259925; PMCID: PMC7785688.

Tandon R, Sharp JS, Zhang F, Pomin VH, Ashpole NM, Mitra D, McCandless MG, Jin W, Liu H, Sharma P, Linhardt RJ. Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives. J Virol. 2021 Jan 13;95(3):e01987-20. doi: 10.1128/JVI.01987-20. PMID: 33173010; PMCID: PMC7925120.

Shofolawe-Bakare OT , Stokes LD , Hossain M , Smith AE , Werfel TA . Immunostimulatory biomaterials to boost tumor immunogenicity. Biomater Sci. 2020 Oct 21;8(20):5516-5537. doi: 10.1039/d0bm01183e. Epub 2020 Sep 2. PMID: 33049007; PMCID: PMC7837217.

Dwivedi R, Pomin VH. Marine Antithrombotics. Mar Drugs. 2020 Oct 13;18(10):514. doi: 10.3390/md18100514. PMID: 33066214; PMCID: PMC7602030.

Liu H, Liang Q, Sharp JS. Peracylation Coupled with Tandem Mass Spectrometry for Structural Sequencing of Sulfated Glycosaminoglycan Mixtures without Depolymerization. J Am Soc Mass Spectrom. 2020 Oct 7;31(10):2061-2072. doi: 10.1021/jasms.0c00178. Epub 2020 Sep 18. PMID: 32902282; PMCID: PMC7664153.

Pandey P, Chatterjee S, Berida T, Doerksen RJ, Roy S. Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening. J Biomol Struct Dyn. 2022 Jul;40(11):4832-4849. doi: 10.1080/07391102.2020.1862705. Epub 2020 Dec 22. PMID: 33353500; PMCID: PMC9948644.