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Focco van den Akker - Publications

Affiliations: 
2003- Biochemistry Case Western Reserve University, Cleveland Heights, OH, United States 
Area:
Biochemistry
Website:
http://www.cwru.edu/med/biochemistry/faculty/vandenakker.html
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61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Mack AR, Kumar V, Taracila MA, Mojica MF, O'Shea M, Schinabeck W, Silver G, Hujer AM, Papp-Wallace KM, Chen S, Haider S, Caselli E, Prati F, van den Akker F, Bonomo RA. Natural protein engineering in the Ω-loop: the role of Y221 in ceftazidime and ceftolozane resistance in -derived cephalosporinase. Antimicrobial Agents and Chemotherapy. e0079123. PMID 37850746 DOI: 10.1128/aac.00791-23  0.491
2023 Kumar V, Boorman J, Greenlee WJ, Zeng X, Lin J, van den Akker F. Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds. Protein Science : a Publication of the Protein Society. e4683. PMID 37209283 DOI: 10.1002/pro.4683  0.469
2023 Zhou HL, Hausladen A, Anand P, Rajavel M, Stomberski CT, Zhang R, Premont RT, Greenlee WJ, van den Akker F, Stamler JS. Identification of a Selective SCoR2 Inhibitor That Protects Against Acute Kidney Injury. Journal of Medicinal Chemistry. PMID 37027003 DOI: 10.1021/acs.jmedchem.2c02089  0.767
2023 Alsenani TA, Rodríguez MM, Ghiglione B, Taracila MA, Mojica MF, Rojas LJ, Hujer AM, Gutkind G, Bethel CR, Rather PN, Introvigne ML, Prati F, Caselli E, Power P, van den Akker F, et al. Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M β-Lactamases: Biochemical and Structural Analyses. Antimicrobial Agents and Chemotherapy. e0093022. PMID 36602311 DOI: 10.1128/aac.00930-22  0.737
2022 Taracila MA, Bethel CR, Hujer AM, Papp-Wallace KM, Barnes MD, Rutter JD, VanPelt J, Shurina BA, van den Akker F, Clancy CJ, Nguyen MH, Cheng S, Shields RK, Page RC, Bonomo RA. Different Conformations Revealed by NMR Underlie Resistance to Ceftazidime/Avibactam and Susceptibility to Meropenem and Imipenem among D179Y Variants of KPC β-Lactamase. Antimicrobial Agents and Chemotherapy. e0212421. PMID 35311523 DOI: 10.1128/aac.02124-21  0.338
2021 Kumar V, Viviani SL, Ismail J, Agarwal S, Bonomo RA, van den Akker F. Structural analysis of the boronic acid β-lactamase inhibitor vaborbactam binding to Pseudomonas aeruginosa penicillin-binding protein 3. Plos One. 16: e0258359. PMID 34653211 DOI: 10.1371/journal.pone.0258359  0.572
2021 Goldberg JA, Kumar V, Spencer EJ, Hoyer D, Marshall SH, Hujer AM, Hujer KM, Bethel CR, Papp-Wallace KM, Perez F, Jacobs MR, van Duin D, Kreiswirth BN, van den Akker F, Plummer MS, et al. A γ-lactam siderophore antibiotic effective against multidrug-resistant Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter spp. European Journal of Medicinal Chemistry. 220: 113436. PMID 33933754 DOI: 10.1016/j.ejmech.2021.113436  0.425
2021 Hahn MG, Lampe T, El Sheikh S, Griebenow N, Woltering E, Schlemmer KH, Dietz L, Gerisch M, Wunder F, Becker-Pelster EM, Mondritzki T, Tinel H, Knorr A, Kern A, Lang D, ... ... van den Akker F, et al. Discovery of the Soluble Guanylate Cyclase Activator Runcaciguat (BAY 1101042). Journal of Medicinal Chemistry. PMID 33872507 DOI: 10.1021/acs.jmedchem.0c02154  0.377
2021 Kumar V, Mathure SA, Lee M, Boorman J, Zeng X, Lin J, Hesek D, Lastochkin E, Mobashery S, van den Akker F. Turnover Chemistry and Structural Characterization of the Cj0843c Lytic Transglycosylase of . Biochemistry. PMID 33749238 DOI: 10.1021/acs.biochem.1c00027  0.402
2021 Rajavel M, Kumar V, Nguyen H, Wyatt J, Marshall SH, Papp-Wallace KM, Deshpande P, Bhavsar S, Yeole R, Bhagwat S, Patel M, Bonomo RA, van den Akker F. Structural Characterization of Diazabicyclooctane β-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. Mbio. 12. PMID 33593978 DOI: 10.1128/mBio.03058-20  0.83
2020 Goldberg J, Nguyen H, Kumar V, Spencer E, Hoyer D, Marshall E, Cmolik A, O'Shea M, Marshall S, Hujer A, Hujer K, Rudin SD, Domitrovic TN, Bethel C, Papp-Wallace KM, ... ... van den Akker F, et al. A γ-Lactam Siderophore Antibiotic Effective Against Multidrug-Resistant Gram-Negative Bacilli. Journal of Medicinal Chemistry. PMID 32420736 DOI: 10.1021/acs.jmedchem.0c00255  0.44
2020 Kumar V, Tang C, Bethel CR, Papp-Wallace KM, Wyatt J, Desarbre E, Bonomo RA, van den Akker F. Structural insights into ceftobiprole inhibition of penicillin-binding protein 3. Antimicrobial Agents and Chemotherapy. PMID 32152075 DOI: 10.1128/AAC.00106-20  0.534
2019 Papp-Wallace KM, Kumar V, Zeiser ET, Becka SA, van den Akker F. Structural Analysis of The OXA-48 Carbapenemase Bound to A "Poor" Carbapenem Substrate, Doripenem. Antibiotics (Basel, Switzerland). 8. PMID 31514291 DOI: 10.3390/antibiotics8030145  0.479
2019 Barnes MD, Kumar V, Bethel CR, Moussa SH, O'Donnell J, Rutter JD, Good CE, Hujer KM, Hujer AM, Marshall SH, Kreiswirth BN, Richter SS, Rather PN, Jacobs MR, Papp-Wallace KM, ... van den Akker F, et al. Targeting Multidrug-Resistant spp.: Sulbactam and the Diazabicyclooctenone β-Lactamase Inhibitor ETX2514 as a Novel Therapeutic Agent. Mbio. 10. PMID 30862744 DOI: 10.1128/Mbio.00159-19  0.506
2018 Vijayaraghavan J, Kumar V, Krishnan NP, Kaufhold RT, Zeng X, Lin J, van den Akker F. Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni. Plos One. 13: e0197136. PMID 29758058 DOI: 10.1371/journal.pone.0197136  0.778
2018 van den Akker F, Bonomo RA. Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine β-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches. Frontiers in Microbiology. 9: 622. PMID 29675000 DOI: 10.3389/fmicb.2018.00622  0.42
2018 Papp-Wallace KM, Nguyen NQ, Jacobs MR, Bethel CR, Barnes MD, Kumar V, Bajaksouzian S, Rudin SD, Rather PN, Bhavsar S, Ravikumar T, Deshpande PK, Patil V, Yeole R, Bhagwat SS, ... ... van den Akker F, et al. Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using β-Lactamase Inhibitors and β-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234. Journal of Medicinal Chemistry. PMID 29627985 DOI: 10.1021/Acs.Jmedchem.8B00091  0.506
2016 Vijayaraghavan J, Kramp K, Harris ME, van den Akker F. Inhibition of soluble guanylyl cyclase by small molecules targeting the catalytic domain. Febs Letters. 590: 3669-3680. PMID 27654641 DOI: 10.1002/1873-3468.12427  0.793
2016 Nguyen NQ, Krishnan NP, Rojas LJ, Prati F, Caselli E, Romagnoli C, Bonomo RA, van den Akker F. Crystal Structures of KPC-2 and SHV-1 β-Lactamases in Complex with the Boronic Acid Transition State Analog S02030. Antimicrobial Agents and Chemotherapy. 60: 1760-6. PMID 26729491 DOI: 10.1128/AAC.02643-15  0.446
2015 Krishnan NP, Nguyen NQ, Papp-Wallace KM, Bonomo RA, van den Akker F. Inhibition of Klebsiella β-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study. Plos One. 10: e0136813. PMID 26340563 DOI: 10.1371/journal.pone.0136813  0.463
2015 Che T, Rodkey EA, Bethel CR, Shanmugam S, Ding Z, Pusztai-Carey M, Nottingham M, Chai W, Buynak JD, Bonomo RA, van den Akker F, Carey PR. Detecting a quasi-stable imine species on the reaction pathway of SHV-1 β-lactamase and 6β-(hydroxymethyl)penicillanic acid sulfone. Biochemistry. 54: 734-43. PMID 25536850 DOI: 10.1021/Bi501197T  0.809
2014 Rodkey EA, Winkler ML, Bethel CR, Pagadala SR, Buynak JD, Bonomo RA, van den Akker F. Penam sulfones and β-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition. Plos One. 9: e85892. PMID 24454944 DOI: 10.1371/Journal.Pone.0085892  0.817
2013 Rodkey EA, McLeod DC, Bethel CR, Smith KM, Xu Y, Chai W, Che T, Carey PR, Bonomo RA, van den Akker F, Buynak JD. β-Lactamase inhibition by 7-alkylidenecephalosporin sulfones: allylic transposition and formation of an unprecedented stabilized acyl-enzyme. Journal of the American Chemical Society. 135: 18358-69. PMID 24219313 DOI: 10.1021/Ja403598G  0.825
2013 von Wantoch Rekowski M, Kumar V, Zhou Z, Moschner J, Marazioti A, Bantzi M, Spyroulias GA, van den Akker F, Giannis A, Papapetropoulos A. Insights into soluble guanylyl cyclase activation derived from improved heme-mimetics. Journal of Medicinal Chemistry. 56: 8948-52. PMID 24090476 DOI: 10.1021/jm400539d  0.448
2013 Kumar V, Martin F, Hahn MG, Schaefer M, Stamler JS, Stasch JP, van den Akker F. Insights into BAY 60-2770 activation and S-nitrosylation-dependent desensitization of soluble guanylyl cyclase via crystal structures of homologous nostoc H-NOX domain complexes. Biochemistry. 52: 3601-8. PMID 23614626 DOI: 10.1021/Bi301657W  0.807
2013 Winkler ML, Rodkey EA, Taracila MA, Drawz SM, Bethel CR, Papp-Wallace KM, Smith KM, Xu Y, Dwulit-Smith JR, Romagnoli C, Caselli E, Prati F, van den Akker F, Bonomo RA. Design and exploration of novel boronic acid inhibitors reveals important interactions with a clavulanic acid-resistant sulfhydryl-variable (SHV) β-lactamase. Journal of Medicinal Chemistry. 56: 1084-97. PMID 23252553 DOI: 10.1021/jm301490d  0.81
2012 Ke W, Pattanaik P, Bethel CR, Sheri A, Buynak JD, Bonomo RA, van den Akker F. Structures of SHV-1 β-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation. Plos One. 7: e49035. PMID 23145056 DOI: 10.1371/Journal.Pone.0049035  0.827
2012 Rodkey EA, Drawz SM, Sampson JM, Bethel CR, Bonomo RA, van den Akker F. Crystal structure of a preacylation complex of the β-lactamase inhibitor sulbactam bound to a sulfenamide bond-containing thiol-β-lactamase. Journal of the American Chemical Society. 134: 16798-804. PMID 22974281 DOI: 10.1021/ja3073676  0.815
2012 Ke W, Laurent AH, Armstrong MD, Chen Y, Smith WE, Liang J, Wright CM, Ostermeier M, van den Akker F. Structure of an engineered β-lactamase maltose binding protein fusion protein: insights into heterotropic allosteric regulation. Plos One. 7: e39168. PMID 22720063 DOI: 10.1371/Journal.Pone.0039168  0.615
2012 Ke W, Rodkey EA, Sampson JM, Skalweit MJ, Sheri A, Pagadala SR, Nottingham MD, Buynak JD, Bonomo RA, van den Akker F. The importance of the trans-enamine intermediate as a β-lactamase inhibition strategy probed in inhibitor-resistant SHV β-lactamase variants. Chemmedchem. 7: 1002-8. PMID 22438274 DOI: 10.1002/Cmdc.201200006  0.802
2012 Ke W, Bethel CR, Papp-Wallace KM, Pagadala SR, Nottingham M, Fernandez D, Buynak JD, Bonomo RA, van den Akker F. Crystal structures of KPC-2 β-lactamase in complex with 3-nitrophenyl boronic acid and the penam sulfone PSR-3-226. Antimicrobial Agents and Chemotherapy. 56: 2713-8. PMID 22330909 DOI: 10.1128/Aac.06099-11  0.624
2011 Baskaran P, Heckler EJ, van den Akker F, Beuve A. Identification of residues in the heme domain of soluble guanylyl cyclase that are important for basal and stimulated catalytic activity. Plos One. 6: e26976. PMID 22096512 DOI: 10.1371/Journal.Pone.0026976  0.314
2011 Sampson JM, Ke W, Bethel CR, Pagadala SR, Nottingham MD, Bonomo RA, Buynak JD, van den Akker F. Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase. Antimicrobial Agents and Chemotherapy. 55: 2303-9. PMID 21357298 DOI: 10.1128/Aac.01360-10  0.817
2011 Ke W, Sampson JM, Ori C, Prati F, Drawz SM, Bethel CR, Bonomo RA, van den Akker F. Novel insights into the mode of inhibition of class A SHV-1 beta-lactamases revealed by boronic acid transition state inhibitors. Antimicrobial Agents and Chemotherapy. 55: 174-83. PMID 21041505 DOI: 10.1128/Aac.00930-10  0.821
2011 van den Akker F, Martin F, Kumar V, Ma X, Stasch J, Schaefer M, Baskaran P, Beuve A, van Dunten PW. Structural insights into sGC activation by different activators Bmc Pharmacology. 11. DOI: 10.1186/1471-2210-11-S1-O11  0.614
2010 Bou G, Santillana E, Sheri A, Beceiro A, Sampson JM, Kalp M, Bethel CR, Distler AM, Drawz SM, Pagadala SR, van den Akker F, Bonomo RA, Romero A, Buynak JD. Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase. Journal of the American Chemical Society. 132: 13320-31. PMID 20822105 DOI: 10.1021/Ja104092Z  0.785
2010 Tsai AL, Berka V, Martin F, Ma X, van den Akker F, Fabian M, Olson JS. Is Nostoc H-NOX a NO sensor or redox switch? Biochemistry. 49: 6587-99. PMID 20572679 DOI: 10.1021/Bi1002234  0.759
2010 Martin F, Baskaran P, Ma X, Dunten PW, Schaefer M, Stasch JP, Beuve A, van den Akker F. Structure of cinaciguat (BAY 58-2667) bound to Nostoc H-NOX domain reveals insights into heme-mimetic activation of the soluble guanylyl cyclase. The Journal of Biological Chemistry. 285: 22651-7. PMID 20463019 DOI: 10.1074/jbc.M110.111559  0.777
2010 Ma X, Beuve A, van den Akker F. Crystal structure of the signaling helix coiled-coil domain of the beta1 subunit of the soluble guanylyl cyclase. Bmc Structural Biology. 10: 2. PMID 20105301 DOI: 10.1186/1472-6807-10-2  0.589
2009 Pattanaik P, Fromondi L, Ng KP, He J, van den Akker F. Expression, purification, and characterization of the intra-cellular domain of the ANP receptor. Biochimie. 91: 888-93. PMID 19393286 DOI: 10.1016/j.biochi.2009.04.011  0.762
2009 Pattanaik P, Bethel CR, Hujer AM, Hujer KM, Distler AM, Taracila M, Anderson VE, Fritsche TR, Jones RN, Pagadala SR, van den Akker F, Buynak JD, Bonomo RA. Strategic design of an effective beta-lactamase inhibitor: LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone. The Journal of Biological Chemistry. 284: 945-53. PMID 18955486 DOI: 10.1074/Jbc.M806833200  0.79
2008 Ma X, Sayed N, Baskaran P, Beuve A, van den Akker F. PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure. The Journal of Biological Chemistry. 283: 1167-78. PMID 18006497 DOI: 10.1074/jbc.M706218200  0.604
2007 Sayed N, Baskaran P, Ma X, van den Akker F, Beuve A. Desensitization of soluble guanylyl cyclase, the NO receptor, by S-nitrosylation. Proceedings of the National Academy of Sciences of the United States of America. 104: 12312-7. PMID 17636120 DOI: 10.1073/pnas.0703944104  0.564
2007 Helfand MS, Taracila MA, Totir MA, Bonomo RA, Buynak JD, van den Akker F, Carey PR. Raman crystallographic studies of the intermediates formed by Ser130Gly SHV, a beta-lactamase that confers resistance to clinical inhibitors. Biochemistry. 46: 8689-99. PMID 17595114 DOI: 10.1021/Bi700581Q  0.314
2007 Ke W, Bethel CR, Thomson JM, Bonomo RA, van den Akker F. Crystal structure of KPC-2: insights into carbapenemase activity in class A beta-lactamases. Biochemistry. 46: 5732-40. PMID 17441734 DOI: 10.1021/Bi700300U  0.539
2007 Ma X, Sayed N, Beuve A, van den Akker F. NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism. The Embo Journal. 26: 578-88. PMID 17215864 DOI: 10.1038/sj.emboj.7601521  0.599
2007 Ma X, Sayed N, Beuve A, van den Akker F. Structural insights into sGC Bmc Pharmacology. 7: S37. DOI: 10.1186/1471-2210-7-s1-s37  0.555
2006 Padayatti PS, Sheri A, Totir MA, Helfand MS, Carey MP, Anderson VE, Carey PR, Bethel CR, Bonomo RA, Buynak JD, van den Akker F. Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 A crystal structure of wt SHV-1 complex with a penam sulfone. Journal of the American Chemical Society. 128: 13235-42. PMID 17017804 DOI: 10.1021/Ja063715W  0.301
2006 Totir MA, Padayatti PS, Helfand MS, Carey MP, Bonomo RA, Carey PR, van den Akker F. Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine beta-lactamase intermediates. Biochemistry. 45: 11895-904. PMID 17002290 DOI: 10.1021/Bi060990M  0.331
2004 Padayatti PS, Pattanaik P, Ma X, van den Akker F. Structural insights into the regulation and the activation mechanism of mammalian guanylyl cyclases. Pharmacology & Therapeutics. 104: 83-99. PMID 15518881 DOI: 10.1016/j.pharmthera.2004.08.003  0.768
2004 Padayatti PS, Helfand MS, Totir MA, Carey MP, Hujer AM, Carey PR, Bonomo RA, van den Akker F. Tazobactam forms a stoichiometric trans-enamine intermediate in the E166A variant of SHV-1 beta-lactamase: 1.63 A crystal structure. Biochemistry. 43: 843-8. PMID 14744126 DOI: 10.1021/Bi035985M  0.316
2000 Chatterjee-Kishore M, van Den Akker F, Stark GR. Adenovirus E1A down-regulates LMP2 transcription by interfering with the binding of stat1 to IRF1. The Journal of Biological Chemistry. 275: 20406-11. PMID 10764778 DOI: 10.1074/Jbc.M001861200  0.438
2000 Chatterjee-Kishore M, van den Akker F, Stark GR. Association of STATs with relatives and friends. Trends in Cell Biology. 10: 106-11. PMID 10675904 DOI: 10.1016/S0962-8924(99)01709-2  0.435
1999 van den Akker F, Hol WG. Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 55: 206-18. PMID 10089411 DOI: 10.1107/S0907444998007161  0.476
1998 Feil IK, Platas AA, van den Akker F, Reddy R, Merritt EA, Storm DR, Hol WG. Stepwise transplantation of an active site loop between heat-labile enterotoxins LT-II and LT-I and characterization of the obtained hybrid toxins. Protein Engineering. 11: 1103-9. PMID 9876933 DOI: 10.1093/protein/11.11.1103  0.497
1998 van den Akker F, Pizza M, Rappuoli R, Hol WG. Crystal structure of a non-toxic mutant of heat-labile enterotoxin, which is a potent mucosal adjuvant. Protein Science : a Publication of the Protein Society. 6: 2650-4. PMID 9416617 DOI: 10.1002/pro.5560061220  0.524
1997 van den Akker F, Feil IK, Roach C, Platas AA, Merritt EA, Hol WG. Crystal structure of heat-labile enterotoxin from Escherichia coli with increased thermostability introduced by an engineered disulfide bond in the A subunit. Protein Science : a Publication of the Protein Society. 6: 2644-9. PMID 9416616 DOI: 10.1002/pro.5560061219  0.492
1996 Feil IK, Reddy R, de Haan L, Merritt EA, van den Akker F, Storm DR, Hol WG. Protein engineering studies of A-chain loop 47-56 of Escherichia coli heat-labile enterotoxin point to a prominent role of this loop for cytotoxicity. Molecular Microbiology. 20: 823-32. PMID 8793878 DOI: 10.1111/j.1365-2958.1996.tb02520.x  0.5
1996 van den Akker F, Steensma E, Hol WG. Tumor marker disaccharide D-Gal-beta 1, 3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli. Protein Science : a Publication of the Protein Society. 5: 1184-8. PMID 8762150 DOI: 10.1002/pro.5560050621  0.438
1995 van den Akker F, Merritt EA, Pizza M, Domenighini M, Rappuoli R, Hol WG. The Arg7Lys mutant of heat-labile enterotoxin exhibits great flexibility of active site loop 47-56 of the A subunit. Biochemistry. 34: 10996-1004. PMID 7669757 DOI: 10.1021/bi00035a005  0.526
1994 Verlinde CL, Merritt EA, Van den Akker F, Kim H, Feil I, Delboni LF, Mande SC, Sarfaty S, Petra PH, Hol WG. Protein crystallography and infectious diseases. Protein Science : a Publication of the Protein Society. 3: 1670-86. PMID 7849584 DOI: 10.1002/Pro.5560031006  0.688
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