The papers co-authored by core CNT3D member labs since 2022:

 

  1. 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
  2. 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.
  3. 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.
  4. 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
  5. 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.
  6. 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
  7. 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
  8. 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.
  9. 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
  10. 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.
  11. 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
  12. 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.
  13. 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.
  14. 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.
  15. 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
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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
  31. 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.
  32. 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.

  33. Eosinophils protect pressure overload- and β-adrenoreceptor agonist-induced cardiac hypertrophy.
    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.
  34. 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.
  35. 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
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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
  41. 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.
  42. 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.

  43. 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

  44. 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

  45. 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.

  46. 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

  47. 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.

  48. 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.

  49. 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.

  50. 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.

  51. 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.