The papers co-authored by core CNT3D member labs since 2022:
- Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer.
Tavakoli N, Fong EJ, Coleman A, Huang YK, Bigger M, Doche ME, Kim S, Lenz HJ, Graham NA, Macklin P, Finley SD, Mumenthaler SM. NPJ Syst Biol Appl. 2025 Jan 28;11(1):12. doi: 10.1038/s41540-025-00494-1. PMID: 39875420 Free PMC article. - Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential.
Wei K, Arlotto M, Overhulse JM, Dinh TA, Zhou Y, Dupper NJ, Yang J, Kashemirov BA, Dawi H, Garnaud C, Bourgine G, Mietton F, Champleboux M, Larabi A, Hayat Y, Indorato RL, Noirclerc-Savoye M, Skoufias D, Cornet M, Rabut G, McKenna CE, Petosa C, Govin J. Adv Sci (Weinh). 2025 Jan 16:e2404260. doi: 10.1002/advs.202404260. Online ahead of print. PMID: 39821709 - Molecular mechanisms of inverse agonism via κ-opioid receptor-G protein complexes.
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Landaker D, Kenakin T, Shenvi R, Majumdar S, Gati C. Nat Chem Biol. 2025 Jan 7. doi: 10.1038/s41589-024-01812-0. Online ahead of print. PMID: 39775170 - An opioid efficacy switch for reversible optical control of peripheral analgesia.
Posa L, Romano G, Ji X, Khan S, Paz BM, Han GW, Nazarova AL, Zaidi SA, Ranjbar M, Pleil K, Katritch V, Gati C, Trauner D, Levitz J. bioRxiv [Preprint]. 2025 Feb 13:2024.12.16.628735. doi: 10.1101/2024.12.16.628735. PMID: 39764058 Free PMC article. Preprint. - Jewel Plummer Cobb: A trailblazing life of impact. Finley SD. Curr Biol. 2024 Dec 16;34(24):R1205-R1211. doi: 10.1016/j.cub.2024.11.008. PMID: 39689683
- Structure-guided design of a peripherally restricted chemogenetic system.
Kang HJ, Krumm BE, Tassou A, Geron M, DiBerto JF, Kapolka NJ, Gumpper RH, Sakamoto K, Dewran Kocak D, Olsen RHJ, Huang XP, Zhang S, Huang KL, Zaidi SA, Nguyen MT, Jo MJ, Katritch V, Fay JF, Scherrer G, Roth BL. Cell. 2024 Dec 26;187(26):7433-7449.e20. doi: 10.1016/j.cell.2024.11.001. Epub 2024 Dec 3. PMID: 39631393 - Structural insights into the high basal activity and inverse agonism of the orphan receptor GPR6 implicated in Parkinson’s disease.
Barekatain M, Johansson LC, Lam JH, Chang H, Sadybekov AV, Han GW, Russo J, Bliesath J, Brice NL, Carlton MBL, Saikatendu KS, Sun H, Murphy ST, Monenschein H, Schiffer HH, Popov P, Lutomski CA, Robinson CV, Liu ZJ, Hua T, Katritch V, Cherezov V. Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. PMID: 39626010 - Nicotinamide Riboside and CD38: Covalent Inhibition and Live-Cell Labeling.
Kao G, Zhang XN, Nasertorabi F, Katz BB, Li Z, Dai Z, Zhang Z, Zhang L, Louie SG, Cherezov V, Zhang Y. JACS Au. 2024 Oct 30;4(11):4345-4360. doi: 10.1021/jacsau.4c00695. eCollection 2024 Nov 25. PMID: 39610739 Free PMC article. - Development of Calcium-Dependent Phospholipase A2 Inhibitors to Target Cellular Senescence and Oxidative Stress in Neurodegenerative Diseases.
Hugo C, Asante I, Sadybekov A, Katritch V, Yassine HN. Antioxid Redox Signal. 2024 Dec;41(16-18):1100-1116. doi: 10.1089/ars.2024.0794. Epub 2024 Nov 22. PMID: 39575710 Review. - Synthesis of USC-093 and comparison with its promoiety enantiomer USC-093D against adenovirus in vitro and in a Syrian hamster model.
Yang J, Riemann SB, Lyu J, Feng S, Bi Y, Lentini NA, Kang I, Kashemirov BA, Hartline CB, James SH, Tollefson AE, Cline-Smith A, Toth K, McKenna CE. bioRxiv [Preprint]. 2024 Nov 1:2024.11.01.621456. doi: 10.1101/2024.11.01.621456. PMID: 39554161 Free PMC article. Preprint. - Decoding Insulin Secretory Granule Maturation Using Genetically Encoded pH Sensors.
Lin W, Tseng K, Fraser SE, Junge J, White KL. ACS Sens. 2024 Nov 22;9(11):6032-6039. doi: 10.1021/acssensors.4c01885. Epub 2024 Nov 6. PMID: 39504473 Free PMC article. - Structure basis of ligand recognition and activation of GPR55.
Chang H, Li X, Shen L, Ge X, Hao S, Wu L, Liu S, Liu J, Cherezov V, Hua T. Cell Res. 2025 Jan;35(1):80-83. doi: 10.1038/s41422-024-01046-8. Epub 2024 Oct 31. PMID: 39482405 No abstract available. - Native mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination.
Kim D, Liu W, Viner R, Cherezov V. Structure. 2024 Dec 5;32(12):2206-2219.e4. doi: 10.1016/j.str.2024.10.004. Epub 2024 Oct 28. PMID: 39471802 - Age-associated imbalance in immune cell regeneration varies across individuals and arises from a distinct subset of stem cells.
Nogalska A, Eerdeng J, Akre S, Vergel-Rodriguez M, Lee Y, Bramlett C, Chowdhury AY, Wang B, Cess CG, Finley SD, Lu R. Cell Mol Immunol. 2024 Dec;21(12):1459-1473. doi: 10.1038/s41423-024-01225-y. Epub 2024 Oct 24. PMID: 39443746 Free PMC article. - Oxa-Iboga alkaloids lack cardiac risk and disrupt opioid use in animal models.
Havel V, Kruegel AC, Bechand B, McIntosh S, Stallings L, Hodges A, Wulf MG, Nelson M, Hunkele A, Ansonoff M, Pintar JE, Hwu C, Ople RS, Abi-Gerges N, Zaidi SA, Katritch V, Yang M, Javitch JA, Majumdar S, Hemby SE, Sames D. Nat Commun. 2024 Sep 20;15(1):8118. doi: 10.1038/s41467-024-51856-y. PMID: 39304653 Free PMC article. - A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site.
Arroyo-Urea S, Nazarova AL, Carrión-Antolí Á, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, García-Nafría J. Nat Commun. 2024 Sep 5;15(1):7759. doi: 10.1038/s41467-024-51993-4. PMID: 39237617 Free PMC article. - Calibrating the Oxidative Capacity of Microdroplets.
Majumder T, Eremin DB, Delibas B, Sarkar A, Fokin V, Dawlaty JM. Angew Chem Int Ed Engl. 2025 Jan 10;64(2):e202414746. doi: 10.1002/anie.202414746. Epub 2024 Oct 30. PMID: 39218788 - Insulator-based dielectrophoresis-assisted separation of insulin secretory vesicles.
Barekatain M, Liu Y, Archambeau A, Cherezov V, Fraser S, White KL, Hayes MA. Elife. 2024 Aug 27;13:e74989. doi: 10.7554/eLife.74989. PMID: 39190030 Free PMC article. - The evolution of computational research in a data-centric world.
Deshpande D, Chhugani K, Ramesh T, Pellegrini M, Shiffman S, Abedalthagafi MS, Alqahtani S, Ye J, Liu XS, Leek JT, Brazma A, Ophoff RA, Rao G, Butte AJ, Moore JH, Katritch V, Mangul S. Cell. 2024 Aug 22;187(17):4449-4457. doi: 10.1016/j.cell.2024.07.045. PMID: 39178828 Review. - Integrating mechanism-based T cell phenotypes into a model of tumor-immune cell interactions.
Tangella N, Cess CG, Ildefonso GV, Finley SD. APL Bioeng. 2024 Aug 20;8(3):036111. doi: 10.1063/5.0205996. eCollection 2024 Sep. PMID: 39175956 Free PMC article. - Monitoring GPCR conformation with GFP-inspired dyes.
Belousov A, Maslov I, Orekhov P, Khorn P, Kuzmichev P, Baleeva N, Motov V, Bogorodskiy A, Krasnova S, Mineev K, Zinchenko D, Zernii E, Ivanovich V, Permyakov S, Hofkens J, Hendrix J, Cherezov V, Gensch T, Mishin A, Baranov M, Mishin A, Borshchevskiy V. iScience. 2024 Jul 4;27(8):110466. doi: 10.1016/j.isci.2024.110466. eCollection 2024 Aug 16. PMID: 39156645 Free PMC article. - Structure-Guided Design of Partial Agonists at an Opioid Receptor.
Che T, Varga B, Bernhard SM, El Daibani A, Zaidi S, Lam J, Aguilar J, Appourchaux K, Nazarova A, Kouvelis A, Eans S, Margolis E, Fay J, Pradhan A, Katritch V, McLaughlin J, Majumdar S. Res Sq [Preprint]. 2024 Jul 16:rs.3.rs-4664764. doi: 10.21203/rs.3.rs-4664764/v1. PMID: 39070616 Free PMC article. Preprint. - Angiotensin-(1-5) is a Potent Endogenous Angiotensin AT 2 -Receptor Agonist.
Souza-Silva IM, Peluso AA, Elsaafien K, Nazarova AL, Assersen KB, Rodrigues-Ribeiro L, Mohammed M, Rodrigues AF, Nawrocki A, Jakobsen LA, Jensen P, de Kloet AD, Krause EG, Borgo MD, Maslov I, Widdop R, Santos RA, Bader M, Larsen M, Verano-Braga T, Katritch V, Sumners C, Steckelings UM. bioRxiv [Preprint]. 2024 Apr 18:2024.04.05.588367. doi: 10.1101/2024.04.05.588367. PMID: 38948791 Free PMC article. Preprint. - Chiral Me-2-arachidonoyl Glycerols: The First Potent Endocannabinoid Glyceride Templates with Stability to COX-2.
Nikas SP, Ji L, Liu Y, Georgiadis MO, Dopeshwarkar A, Straiker A, Kudalkar S, Sadybekov AV, Dvorakova M, Katritch V, Mackie K, Marnett L, Makriyannis A. ACS Med Chem Lett. 2024 May 28;15(6):965-971. doi: 10.1021/acsmedchemlett.4c00175. eCollection 2024 Jun 13. PMID: 38894922 - Visualizing partial solvation at the air-water interface.
Judd KD, Parsons SW, Eremin DB, Fokin VV, Dawlaty JM.Chem Sci. 2024 Apr 24;15(22):8346-8354. doi: 10.1039/d4sc01311e. eCollection 2024 Jun 5.PMID: 38846382 Free PMC article. - Modeling the heterogeneous apoptotic response of caspase-mediated signaling in tumor cells.
Mangrum DS, Finley SD. J Theor Biol. 2024 Aug 7;590:111857. doi: 10.1016/j.jtbi.2024.111857. Epub 2024 May 24. PMID: 38797470 - Merging Metabolic Modeling and Imaging for Screening Therapeutic Targets in Colorectal Cancer.
Tavakoli N, Fong EJ, Coleman A, Huang YK, Bigger M, Doche ME, Kim S, Lenz HJ, Graham NA, Macklin P, Finley SD, Mumenthaler SM. bioRxiv [Preprint]. 2024 Dec 5:2024.05.24.595756. doi: 10.1101/2024.05.24.595756.
Update in: NPJ Syst Biol Appl. 2025 Jan 28;11(1):12. doi: 10.1038/s41540-025-00494-1. PMID: 38826317 Free PMC article. Preprint. - Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography.
Deshmukh A, Chang K, Cuala J, Vanslembrouck B, Georgia S, Loconte V, White KL.Cells. 2024 May 18;13(10):869. doi: 10.3390/cells13100869.PMID: 38786091 Free PMC article. - Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β.
Alnajjar KS, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. Biochemistry. 2024 Jun 4;63(11):1412-1422. doi: 10.1021/acs.biochem.4c00065. Epub 2024 May 23. PMID: 38780930 - ONE-GO: Direct detection of context-dependent GPCR activity.
Raskovalov A, Kim D, Cherezov V. Cell Res. 2024 Aug; 34(8):543-544. doi: 10.1038/s41422-024-00966-9. PMID: 38688989 No abstract available. - Scalable computation of anisotropic vibrations for large macromolecular assemblies.
Lam JH, Nakano A, Katritch V. Nat Commun. 2024 Apr 24;15(1):3479. doi: 10.1038/s41467-024-47685-8. PMID: 38658556 Free PMC article. - Integrating Diversity, Equity, and Inclusion into Preclinical, Clinical, and Public Health Mathematical Models.
Sheen J, Curtin L, Finley S, Konstorum A, McGee R, Craig M. Bull Math Biol. 2024 Apr 16;86(5):56. doi: 10.1007/s11538-024-01282-4. PMID: 38625656 Free PMC article. - Virtual Screening of a Chemically Diverse “Superscaffold” Library Enables Ligand Discovery for a Key GPCR Target.
Grotsch K, Sadybekov AV, Hiller S, Zaidi S, Eremin D, Le A, Liu Y, Smith EC, Illiopoulis-Tsoutsouvas C, Thomas J, Aggarwal S, Pickett JE, Reyes C, Picazo E, Roth BL, Makriyannis A, Katritch V, Fokin VV. ACS Chem Biol. 2024 Apr 19;19(4):866-874. doi: 10.1021/acschembio.3c00602. Epub 2024 Apr 10. PMID: 38598723 - Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach.
Rao S, Sadybekov A, DeWitt DC, Lipka J, Katritch V, Herring BE. Mol Autism. 2024 Apr 3;15(1):12. doi: 10.1186/s13229-024-00590-9. PMID: 38566250 Free PMC article. - Novel bisphosphonate-based cathepsin K-triggered compound targets the enthesis without impairing soft tissue-to-bone healing.
Shi BY, Sriram V, Wu SY, Huang D, Cheney A, Metzger MF, Sundberg O, Lyons KM, McKenna CE, Nishimura I, Kremen TJ Jr. Front Bioeng Biotechnol. 2024 Feb 16;12:1308161. doi: 10.3389/fbioe.2024.1308161. eCollection 2024. PMID: 38433822 Free PMC article. - In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography.
Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. Nat Commun. 2024 Feb 12;15(1):1311. doi: 10.1038/s41467-024-45648-7. PMID: 38346988 Free PMC article. - Constitutive activation mechanism of a class C GPCR.
Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y. Nat Struct Mol Biol. 2024 Apr;31(4):678-687. doi: 10.1038/s41594-024-01224-7. Epub 2024 Feb 8. PMID: 38332368 - Flux sampling in genome-scale metabolic modeling of microbial communities.
Gelbach PE, Cetin H, Finley SD. BMC Bioinformatics. 2024 Jan 29;25(1):45. doi: 10.1186/s12859-024-05655-3. PMID: 38287239 Free PMC article. - Uridine Bisphosphonates Differentiate Phosphoglycosyl Transferase Superfamilies.
Seebald LM, Haratipour P, Jacobs MR, Bernstein HM, Kashemirov BA, McKenna CE, Imperiali B. J Am Chem Soc. 2024 Feb 7;146(5):3220-3229. doi: 10.1021/jacs.3c11402. Epub 2024 Jan 25. PMID: 38271668 Free PMC article. - Packaging monoamine neurotransmitters.
Yadav R, Gati C. Cell Res. 2024 Mar;34(3):185-186. doi: 10.1038/s41422-023-00922-z. PMID: 38242944 No abstract available. - Oral USC-093, a novel homoserinamide analogue of the tyrosinamide (S)-HPMPA prodrug USC-087 has decreased nephrotoxicity while maintaining antiviral efficacy against human adenovirus infection of Syrian hamsters.
Tollefson AE, Riemann SB, Ying B, Spencer JF, Overhulse JM, Kashemirov BA, Wold WSM, McKenna CE, Toth K. Antiviral Res. 2024 Feb;222:105799. doi: 10.1016/j.antiviral.2024.105799. Epub 2024 Jan 6. PMID: 38190973 Free PMC article. - Development of an automated, high-throughput assay to detect angiotensin AT2-receptor agonistic compounds by nitric oxide measurements in vitro.
Souza-Silva IM, Peluso AA, Mortensen C, Nazarova AL, Stage TB, Sumners C, Katritch V, Steckelings UM. Peptides. 2024 Feb;172:171137. doi: 10.1016/j.peptides.2023.171137. Epub 2023 Dec 22. PMID: 38142816 - Flux sampling in genome-scale metabolic modeling of microbial communities.
Gelbach PE, Cetin H, Finley SD.BMC Bioinformatics. 2024 Jan 29;25(1):45. doi: 10.1186/s12859-024-05655-3.PMID: 38287239 - Packaging monoamine neurotransmitters.
Yadav R, Gati C.Cell Res. 2024 Jan 19. doi: 10.1038/s41422-023-00922-z. Online ahead of print.PMID: 38242944 No abstract available. - Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket.
Arroyo-Urea S, Nazarova AL, Carrión-Antolí Á, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, García-Nafría J.Res Sq. 2023 Dec 19:rs.3.rs-3433207. doi: 10.21203/rs.3.rs-3433207/v1. Preprint.PMID: 38196573 Free PMC article. - Development of an automated, high-throughput assay to detect angiotensin AT2-receptor agonistic compounds by nitric oxide measurements in vitro.
Souza-Silva IM, Peluso AA, Mortensen C, Nazarova AL, Stage TB, Sumners C, Katritch V, Steckelings UM.Peptides. 2024 Feb;172:171137. doi: 10.1016/j.peptides.2023.171137. Epub 2023 Dec 22.PMID: 38142816 - Information-Theoretic Analysis of a Model of CAR-4-1BB-Mediated NFκB Activation.
Tserunyan V, Finley S.Bull Math Biol. 2023 Dec 1;86(1):5. doi: 10.1007/s11538-023-01232-6. PMID: 38038772 Free PMC article. - Molecular basis of anaphylatoxin binding, activation, and signaling bias at complement receptors.
Yadav MK, Maharana J, Yadav R, Saha S, Sarma P, Soni C, Singh V, Saha S, Ganguly M, Li XX, Mohapatra S, Mishra S, Khant HA, Chami M, Woodruff TM, Banerjee R, Shukla AK, Gati C.Cell. 2023 Oct 26;186(22):4956-4973.e21. doi: 10.1016/j.cell.2023.09.020. Epub 2023 Oct 17. PMID: 37852260 - Generation and Aerobic Oxidation of Azavinyl Captodative Radicals.
Aggarwal S, Richards WJ, Fokin VV.J Am Chem Soc. 2023 Sep 21. doi: 10.1021/jacs.3c06068. Online ahead of print. PMID: 37733969 - Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer.
Gelbach PE, Finley SD.iScience. 2023 Aug 9;26(9):107569. doi: 10.1016/j.isci.2023.107569. eCollection 2023 Sep 15. PMID: 37664588 Free PMC article. - Synthesis and anti-cancer potential of potent peripheral MAOA inhibitors designed to limit blood:brain penetration.
Jacobs MR, Olivero JE, Ok Choi H, Liao CP, Kashemirov BA, Katz JE, Gross ME, McKenna CE.Bioorg Med Chem. 2023 Sep 7;92:117425. doi: 10.1016/j.bmc.2023.117425. Epub 2023 Jul 26. PMID: 37544256 - A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion.
Ildefonso GV, Finley SD.NPJ Syst Biol Appl. 2023 Jul 31;9(1):36. doi: 10.1038/s41540-023-00297-2. PMID: 37524735 Free PMC article. - Pharmacological and Physicochemical Properties Optimization for Dual-Target Dopamine D3 (D3R) and μ-Opioid (MOR) Receptor Ligands as Potentially Safer Analgesics.
Bonifazi A, Saab E, Sanchez J, Nazarova AL, Zaidi SA, Jahan K, Katritch V, Canals M, Lane JR, Newman AH.J Med Chem. 2023 Aug 10;66(15):10304-10341. doi: 10.1021/acs.jmedchem.3c00417. Epub 2023 Jul 19. PMID: 37467430 - Information-theoretic analysis of a model of CAR-4-1BB-mediated NFκB activation.
Tserunyan V, Finley S.bioRxiv. 2023 Jun 10:2023.06.09.544433. doi: 10.1101/2023.06.09.544433. Preprint. PMID: 37333129 Free PMC article. Updated. - Decoding the mechanisms of allostery.
Khan S, Gati C.Elife. 2023 Jun 2;12:e88749. doi: 10.7554/eLife.88749. PMID: 37265322 Free PMC article. - A systems and computational biology perspective on advancing CAR therapy.
Tserunyan V, Finley SD.Semin Cancer Biol. 2023 Sep;94:34-49. doi: 10.1016/j.semcancer.2023.05.009. Epub 2023 May 30. PMID: 37263529 Review. - Arenes participate in 1,3-dipolar cycloaddition with in situ-generated diazoalkenes.
Aggarwal S, Vu A, Eremin DB, Persaud R, Fokin VV.Nat Chem. 2023 Jun;15(6):764-772. doi: 10.1038/s41557-023-01188-z. Epub 2023 May 22. PMID: 37217789 - Ligand and G-protein selectivity in the κ-opioid receptor.
Han J, Zhang J, Nazarova AL, Bernhard SM, Krumm BE, Zhao L, Lam JH, Rangari VA, Majumdar S, Nichols DE, Katritch V, Yuan P, Fay JF, Che T.Nature. 2023 May;617(7960):417-425. doi: 10.1038/s41586-023-06030-7. Epub 2023 May 3. PMID: 37138078 Free PMC article. - Microwave-Accelerated McKenna Synthesis of Phosphonic Acids: An Investigation.
Mustafa D, Overhulse JM, Kashemirov BA, McKenna CE.Molecules. 2023 Apr 15;28(8):3497. doi: 10.3390/molecules28083497. PMID: 37110732 Free PMC article. - Computational approaches streamlining drug discovery.
Sadybekov AV, Katritch V.Nature. 2023 Apr;616(7958):673-685. doi: 10.1038/s41586-023-05905-z. Epub 2023 Apr 26. PMID: 37100941 Review. - Calibrating agent-based models to tumor images using representation learning.
Cess CG, Finley SD.PLoS Comput Biol. 2023 Apr 21;19(4):e1011070. doi: 10.1371/journal.pcbi.1011070. eCollection 2023 Apr. PMID: 37083821 Free PMC article. - Structural insights into angiotensin receptor signaling modulation by balanced and biased agonists.
Zhang D, Liu Y, Zaidi SA, Xu L, Zhan Y, Chen A, Guo J, Huang XP, Roth BL, Katritch V, Cherezov V, Zhang H.EMBO J. 2023 Jun 1;42(11):e112940. doi: 10.15252/embj.2022112940. Epub 2023 Apr 11. PMID: 37038975 - Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells.
Aydin Y, Böttke T, Lam JH, Ernicke S, Fortmann A, Tretbar M, Zarzycka B, Gurevich VV, Katritch V, Coin I.Nat Commun. 2023 Mar 1;14(1):1151. doi: 10.1038/s41467-023-36797-2. PMID: 36859440 Free PMC article. - Molecular mechanism of biased signaling at the kappa opioid receptor.
El Daibani A, Paggi JM, Kim K, Laloudakis YD, Popov P, Bernhard SM, Krumm BE, Olsen RHJ, Diberto J, Carroll FI, Katritch V, Wünsch B, Dror RO, Che T.Nat Commun. 2023 Mar 11;14(1):1338. doi: 10.1038/s41467-023-37041-7. PMID: 36906681 Free PMC article. - Pharmacological Mechanism of the Non-hallucinogenic 5-HT2A Agonist Ariadne and Analogs.
Cunningham MJ, Bock HA, Serrano IC, Bechand B, Vidyadhara DJ, Bonniwell EM, Lankri D, Duggan P, Nazarova AL, Cao AB, Calkins MM, Khirsariya P, Hwu C, Katritch V, Chandra SS, McCorvy JD, Sames D.ACS Chem Neurosci. 2023 Jan 4;14(1):119-135. doi: 10.1021/acschemneuro.2c00597. Epub 2022 Dec 15. PMID: 36521179 Free PMC article. - Structure-based design of bitopic ligands for the µ-opioid receptor.
Faouzi A, Wang H, Zaidi SA, DiBerto JF, Che T, Qu Q, Robertson MJ, Madasu MK, El Daibani A, Varga BR, Zhang T, Ruiz C, Liu S, Xu J, Appourchaux K, Slocum ST, Eans SO, Cameron MD, Al-Hasani R, Pan YX, Roth BL, McLaughlin JP, Skiniotis G, Katritch V, Kobilka BK, Majumdar S.Nature. 2023 Jan;613(7945):767-774. doi: 10.1038/s41586-022-05588-y. Epub 2022 Nov 30. PMID: 36450356 Free PMC article. - Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion.
Gelbach PE, Zheng D, Fraser SE, White KL, Graham NA, Finley SD.PLoS Comput Biol. 2022 Oct 17;18(10):e1010555. doi: 10.1371/journal.pcbi.1010555. eCollection 2022 Oct. PMID: 36251711 Free PMC article. - Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding.
Zhou Y, Overhulse JM, Dupper NJ, Guo Y, Kashemirov BA, Wei K, Govin J, Petosa C, McKenna CE.J Comput Chem. 2022 Dec 15;43(32):2121-2130. doi: 10.1002/jcc.26997. Epub 2022 Oct 3. PMID: 36190786 Free PMC article. - GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor.
Shiriaeva A, Park D, Kim G, Lee Y, Hou X, Jarhad DB, Kim G, Yu J, Hyun YE, Kim W, Gao ZG, Jacobson KA, Han GW, Stevens RC, Jeong LS, Choi S, Cherezov V.J Med Chem. 2022 Sep 8;65(17):11648-11657. doi: 10.1021/acs.jmedchem.2c00462. Epub 2022 Aug 17. PMID: 35977382 Free PMC article. - Structural basis for receptor selectivity and inverse agonism in S1P5 receptors.
Lyapina E, Marin E, Gusach A, Orekhov P, Gerasimov A, Luginina A, Vakhrameev D, Ergasheva M, Kovaleva M, Khusainov G, Khorn P, Shevtsov M, Kovalev K, Bukhdruker S, Okhrimenko I, Popov P, Hu H, Weierstall U, Liu W, Cho Y, Gushchin I, Rogachev A, Bourenkov G, Park S, Park G, Hyun HJ, Park J, Gordeliy V, Borshchevskiy V, Mishin A, Cherezov V.Nat Commun. 2022 Aug 12;13(1):4736. doi: 10.1038/s41467-022-32447-1. PMID: 35961984 Free PMC article. - Inhibition of the angiotensin II type 2 receptor AT2R is a novel therapeutic strategy for glioblastoma.
Perryman R, Renziehausen A, Shaye H, Kostagianni AD, Tsiailanis AD, Thorne T, Chatziathanasiadou MV, Sivolapenko GB, El Mubarak MA, Han GW, Zarzycka B, Katritch V, Lebon G, Lo Nigro C, Lattanzio L, Morse SV, Choi JJ, O’Neill K, Kanaki Z, Klinakis A, Crook T, Cherezov V, Tzakos AG, Syed N.Proc Natl Acad Sci U S A. 2022 Aug 9;119(32):e2116289119. doi: 10.1073/pnas.2116289119. Epub 2022 Aug 2. PMID: 35917342 Free PMC article. - Crystallization of Microbial Rhodopsins.
Kovalev K, Astashkin R, Gordeliy V, Cherezov V.Methods Mol Biol. 2022;2501:125-146. doi: 10.1007/978-1-0716-2329-9_6. PMID: 35857226 - Inactive and active state structures template selective tools for the human 5-HT5A receptor.
Zhang S, Chen H, Zhang C, Yang Y, Popov P, Liu J, Krumm BE, Cao C, Kim K, Xiong Y, Katritch V, Shoichet BK, Jin J, Fay JF, Roth BL.Nat Struct Mol Biol. 2022 Jul;29(7):677-687. doi: 10.1038/s41594-022-00796-6. Epub 2022 Jul 14. PMID: 35835867 Free PMC article. - Structural basis of GABA reuptake inhibition. Motiwala Z, Aduri NG, Shaye H, Han GW, Lam JH, Katritch V, Cherezov V, Gati C.Nature. 2022 Jun;606(7915):820-826. doi: 10.1038/s41586-022-04814-x. Epub 2022 Jun 8. PMID: 35676483 Free PMC article.
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Yang C, Li J, Deng Z, Luo S, Liu J, Fang W, Liu F, Liu T, Zhang X, Zhang Y, Meng Z, Zhang S, Luo J, Liu C, Yang D, Liu L, Sukhova GK, Sadybekov A, Katritch V, Libby P, Wang J, Guo J, Shi GP.Cardiovasc Res. 2023 Mar 17;119(1):195-212. doi: 10.1093/cvr/cvac060. PMID: 35394031 Free PMC article. - It all clicks together: In silico drug discovery becoming mainstream.
Nazarova AL, Katritch V.Clin Transl Med. 2022 Apr;12(4):e766. doi: 10.1002/ctm2.766. PMID: 35377970 Free PMC article. No abstract available. - Phosphatases are predicted to govern prolactin-mediated JAK-STAT signaling in pancreatic beta cells.
Simoni AD, Huber HA, Georgia SK, Finley SD.Integr Biol (Camb). 2022 Apr 8;14(2):37-48. doi: 10.1093/intbio/zyac004. PMID: 35368075 - Between Science and Big Business: Tapping Mary Jane’s Uncharted Potential.
Grotsch K, Fokin VV.ACS Cent Sci. 2022 Feb 23;8(2):156-168. doi: 10.1021/acscentsci.1c01100. Epub 2022 Jan 26. PMID: 35233448 Free PMC article. Review. - Schizophrenia-associated SAP97 mutations increase glutamatergic synapse strength in the dentate gyrus and impair contextual episodic memory in rats.
Kay Y, Tsan L, Davis EA, Tian C, Décarie-Spain L, Sadybekov A, Pushkin AN, Katritch V, Kanoski SE, Herring BE.Nat Commun. 2022 Feb 10;13(1):798. doi: 10.1038/s41467-022-28430-5. PMID: 35145085 Free PMC article. - Synthon-based ligand discovery in virtual libraries of over 11 billion compounds
Sadybekov AA, Sadybekov AV, Liu Y, Iliopoulos-Tsoutsouvas C, Huang XP, Pickett J, Houser B, Patel N, Tran NK, Tong F, Zvonok N, Jain MK, Savych O, Radchenko DS, Nikas SP, Petasis NA, Moroz YS, Roth BL, Makriyannis A, Katritch V.Nature. 2022 Jan;601(7893):452-459. doi: 10.1038/s41586-021-04220-9. Epub 2021 Dec 15. PMID: 34912117 Free PMC article. - Mechanistic characterization of endothelial sprouting mediated by pro-angiogenic signaling.
Song M, Finley SD.Microcirculation. 2022 Feb;29(2):e12744. doi: 10.1111/micc.12744. Epub 2021 Dec 28. PMID: 34890488 Free PMC article. - Dual Electrospray Ionization Enhancement of Proteins Enabled by DMSO Supercharging Reagent.
Eremin DB, Fokin VV.J Am Soc Mass Spectrom. 2022 Jan 5;33(1):203-206. doi: 10.1021/jasms.1c00280. Epub 2021 Dec 1. PMID: 34850625 - Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics.
Wang J, Delfarah A, Gelbach PE, Fong E, Macklin P, Mumenthaler SM, Graham NA, Finley SD.Metab Eng. 2022 Jan;69:175-187. doi: 10.1016/j.ymben.2021.11.006. Epub 2021 Nov 25. PMID: 34838998 Free PMC article. - Structural Characterization of KOR Inactive and Active States for 3D Pharmacology and Drug Discovery.
Zaidi SA, Katritch V.Handb Exp Pharmacol. 2022;271:41-64. doi: 10.1007/164_2021_461. PMID: 33945028 Review. - Uridine Bisphosphonates Differentiate Phosphoglycosyl Transferase Superfamilies.
Seebald LM, Haratipour P, Jacobs MR, Bernstein HM, Kashemirov BA, McKenna CE, Imperiali B.J Am Chem Soc. 2024 Jan 25. doi: 10.1021/jacs.3c11402. Online ahead of print. PMID: 38271668 - Oral USC-093, a novel homoserinamide analogue of the tyrosinamide (S)-HPMPA prodrug USC-087 has decreased nephrotoxicity while maintaining antiviral efficacy against human adenovirus infection of Syrian hamsters.
Tollefson AE, Riemann SB, Ying B, Spencer JF, Overhulse JM, Kashemirov BA, Wold WSM, McKenna CE, Toth K.Antiviral Res. 2024 Jan 6;222:105799. doi: 10.1016/j.antiviral.2024.105799. Online ahead of print. PMID: 38190973 - MicroED structure of the human vasopressin 1B receptor.
Shiriaeva A, Martynowycz MW, Nicolas WJ, Cherezov V, Gonen T.bioRxiv. 2023 Jul 6:2023.07.05.547888. doi: 10.1101/2023.07.05.547888. Preprint. PMID: 37461729 Free PMC article. - Biologically-coupled bisphosphonate chaperones effectively deliver molecules to the site of soft tissue-bone healing.
Kremen TJ Jr, Shi BY, Wu SY, Sundberg O, Sriram V, Kim W, Sheyn D, Lyons KM, Wang W, McKenna CE, Nishimura I.J Orthop Res. 2023 Oct;41(10):2250-2260. doi: 10.1002/jor.25579. Epub 2023 May 8. PMID: 37087676 - Serial femtosecond crystallography.
Barends TRM, Stauch B, Cherezov V, Schlichting I.Nat Rev Methods Primers. 2022 Aug 4;2:59. doi: 10.1038/s43586-022-00141-7. PMID: 36643971 Free PMC article. - Electrochemical Studies of the Cycloaddition Activity of Bismuth(III) Acetylides Towards Organic Azides Under Copper(I)-Catalyzed Conditions.
Nazarova AL, Zayat B, Fokin VV, Narayan SR.Front Chem. 2022 Feb 25;10:830237. doi: 10.3389/fchem.2022.830237. eCollection 2022. PMID: 36204144 Free PMC article. - Fluorescent risedronate analogue 800CW-pRIS improves tooth extraction-associated abnormal wound healing in zoledronate-treated mice.
Okawa H, Kondo T, Hokugo A, Cherian P, Sundberg O, Campagna JJ, Kashemirov BA, John V, Sun S, Ebetino FH, McKenna CE, Nishimura I.Commun Med (Lond). 2022 Sep 5;2:112. doi: 10.1038/s43856-022-00172-x. eCollection 2022. PMID: 36082175 Free PMC article. - Oral microbial extracellular DNA initiates periodontitis through gingival degradation by fibroblast-derived cathepsin K in mice.
Kondo T, Okawa H, Hokugo A, Shokeen B, Sundberg O, Zheng Y, McKenna CE, Lux R, Nishimura I.Commun Biol. 2022 Sep 14;5(1):962. doi: 10.1038/s42003-022-03896-7. PMID: 36104423 Free PMC article. - Mechanism of bisphosphonate-related osteonecrosis of the jaw (BRONJ) revealed by targeted removal of legacy bisphosphonate from jawbone using competing inert hydroxymethylene diphosphonate.
Okawa H, Kondo T, Hokugo A, Cherian P, Campagna JJ, Lentini NA, Sung EC, Chiang S, Lin YL, Ebetino FH, John V, Sun S, McKenna CE, Nishimura I.Elife. 2022 Aug 26;11:e76207. doi: 10.7554/eLife.76207. PMID: 36017995 Free PMC article.