The van den Akker Lab

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Recent publications
  • Rajavel, M., Kumar, V., Nguyen, H., Wyatt, J., Marshall, S.H., Papp-Wallace, K.M., Deshpande, P., Bhavsar, S., Yeole, R., Bhagwat, S.S., Patel, M., Bonomo, R.A., van den Akker, F. “ Structural characterization of diazabicyclooctane β-lactam "enhancers" bound to penicillin-binding proteins PBP2 and PBP3 of Pseudomonas aeruginosa. ” mBio 2021, 12(1):e03058-20 Read article in Pubmed
  • Goldberg, J., Nguyen, H., Kumar, V., Spencer, E., Hoyer, D., Marshall, E., Cmolik, A., O’Shea, M., Marshall, S., Hujer, A., Hujer, K., Rudin, S.D., Domitrovic, T.N., Bethel, C., Papp-Wallace, K.M., Logan, L., Perez, F., Jacobs, M., van Duin, D., Kreiswirth, B., Bonomo, R.A.*, Plummer, M.*, van den Akker, F.* “ A γ-Lactam Siderophore Antibiotic Effective Against Multidrug-Resistant Gram-Negative Bacilli. ” J. Med. Chem. 2020, 63, 5990-6002 Read article in Pubmed
  • Kumar, V., Tang, C., Bethel C.R., Papp-Wallace K.M., Wyatt, J., Desarbre, E., Bonomo, R.A., van den Akker F. “ Structural insights into ceftobiprole inhibition of Pseudomonas aeruginosa penicillin-binding protein 3. ” Antimicrob Agents Chemother. 2020, ePub 3/9/20 Read article in Pubmed
  • Papp-Wallace, K.M.*, Kumar, V., Zeiser, E.T., Becka, S.A., van den Akker F.* “ Structural Analysis of The OXA-48 Carbapenemase Bound to A "Poor" Carbapenem Substrate, Doripenem. ” Antibiotics 2019, 8, pii: E145 Read article in PubMed
  • Mesiano, S.A., Peters, G.A., Amini, P., Wilson, R.A., Tochtrop, G.P., van den Akker. F. “ Progestin therapy to prevent preterm birth: History and effectiveness of current strategies and development of novel approaches. ” Placenta 2019, 46-52 Read article in PubMed
  • Barnes, M.D., Kumar, V., Bethel, C.R., Moussa, S.H., O’Donnell, J., Rutter, J.D., Good, C.E., Hujer, K.M., Hujer, A.M., Marshall, S.H., Kreiswirth, B.N., Richter, S.S., Rather, P.N., Jacobs, M.R., Papp-Wallace, K.M., van den Akker, F.*, Bonomo, R.A.* “ Targeting Multidrug-Resistant Acinetobacter spp.: Sulbactam and the Diazabicyclooctenone β-Lactamase Inhibitor ETX2514 as a Novel Therapeutic Agent. ” mBio 2019, e00159-19. Read article in PubMed
  • Stomberski, C.T., Zhou, H.-L., Wang, L., van den Akker, F., Stamler, J.S. “ Molecular recognition of S-nitrosothiol substrate by its cognate protein denitrosylase. ” J. Biol. Chem. 2018, 294, 1568-1578. Read article in PubMed
  • Vijayaraghavan, J., Kumar, V., Krishnan, N.P., Kaufhold, R.T., 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 2018, e0197136. Read article in PubMed
  • Papp-Wallace, K.M.*, Nguyen, N.Q., Jacobs, M.R., Bethel, C.R., Barnes, M.D., Kumar, V., Bajaksouzian, S., Rudin, S.D., Bhavsar, S., Ravikumar, T., Deshpande, P.K., Patil, V., Yeole, R., Bhagwat, S.S., Patel, M.V., van den Akker, F.*, Bonomo, R.A.* “ Strategic approaches to overcome resistance against Gram negative pathogens using beta-lactamase inhibitors and beta-lactam enhancers: The activity of three novel diazabicyclooctanes, zidebactam (WCK 5107), WCK 5153, WCK 4234. ” J. Med. Chem 2018, 61, 4067-4086. Read article in PubMed
  • van den Akker, F.*, Bonomo, R.A. “ Exploring additional dimensions of complexity in inhibitor design for serine beta-lactamases: mechanistic and intra- and inter-moleculra chemistry approach. ” Front Microbiol. 2018, 9, 622. Read article in PubMed
  • Chen A., Tiosano, D., Guran, T., Baris, H.N., Bayram, Y., Mory, A., Shapiro-Kulnane, L., Hodges, C.A., Coban Akdemir, Z., Turan, S., Jhangiani, S.N., van den Akker, F., Hoppel, C.L., Salz, H.K., Lupski, J.R., Buchner, D.A. “ Mutations in the mitochondrial ribosomal protein MRPS22 lead to primary ovarian insufficiency. ” Hum Mol. Genet. 2018, 27, 1913-1926. Read article in PubMed
  • Nguyen N.Q., Krishnan N.P., Rojas L.J., Prati F., Caselli E., Romagnoli C., Bonomo R.A., van den Akker F. “ Crystal structures of KPC-2 and SHV-1 beta-lactamases in complex with the boronic acid transition state analog S02030. ” Antimicrob Agents Chemother. 2016, 60, 1760-6. Read article in PubMed
  • Krishnan N.P., Nguyen N.Q., Papp-Wallace K.M., Bonomo R.A., van den Akker F. “ Inhibition of Klebsiella beta-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study. ” Plos One Sep 4;10(9):e0136813 (2015) Read article in PubMed
  • Rodkey E.A., Winkler, M.L., Bethel C.R., Pagadala, S.R.R., Buynak, J.D., Bonomo R.A., van den Akker F. “Penam sulfones and beta-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition. ” Plos One Epub Jan 16 (2014) Read article in PubMed
  • Rodkey E.A., McLeod D.C., Bethel C.R., Smith K.M., Xu Y., Chai W., Che T., Carey P.R., Bonomo R.A., van den Akker F., Buynak J.D. “beta-Lactamase Inhibition by 7-Alkylidenecephalosporin Sulfones: Allylic Transposition and Formation of an Unprecedented Stabilized Acyl-Enzyme. ” J. Am. Chem. Soc. Epub Dec 3(2013) Read article in PubMed
  • von Wantoch Rekowski M., Kumar V., Zhou Z., Moschner J., Marazioti A., Bantzi M., Spyroulias G.A., van den Akker F., Giannis A., Papapetropoulos A. “Insights into Soluble Guanylyl Cyclase Activation Derived from Improved Heme-Mimetics. ” J. Med. Chem. Epub Oct 24(2013) Read article in PubMed
  • Kumar V., Martin F.E., Hahn M.G., Schaefer M., Stamler J.S., Stasch J.P., 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 Epub Apr 24 (2013) Read article in PubMed
  • Ke W., Pattanaik P., Bethel C.R., Sheri A., Buynak J.D., Bonomo R.A., van den Akker F. “Structures of SHV-1 beta-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation.” Plos One e49035 (2012) Read article in PubMed
  • Rodkey E.A., Drawz S.M., Sampson J.M. Bethel C.R., Bonomo R.A., and van den Akker F. “Crystal structure of a pre-acylation complex of the beta-lactamase inhibitor, sulbactam, bound to a sulfenamide bond containing thiol-beta-lactamase ” J. Am. Chem. Soc. epub Sep 26, (2012) Read article in PubMed
  • Ke W., Laurent A.H., Armstrong M.D., Chen Y., Smith W.E., Liang J., Wright C.M., Ostermeier M., and van den Akker F. “Structure of an Engineered beta-Lactamase Maltose Binding Protein Fusion Protein: Insights into Heterotropic Allosteric Regulation ” Plos One 7: e39168 (2012) Read article in PubMed
  • Ke W, Rodkey R.A., Sampson J.M., Skalweit M.J., Sheri A., Pagadala S.R.R., Nottingham M.D., Buynak J.D., Bonomo R.A., van den Akker F. “The importance of the trans-enamine intermediate as a beta-lactamase inhibition strategy probed in inhibitor-resistant SHV beta-lactamase variants” ChemMedChem 7: 1002-1008 (2012) Read article in PubMed
  • Ke W., Bethel C.R., Papp-Wallace K.M., Pagadala S.R., Nottingham M., Fernandez D., Buynak J.D., Bonomo R.A., van den Akker F. “Crystal structures of KPC-2 beta-lactamase in complex with 3-NPBA and PSR-3-226” Antimicrob Agents Chemother ePub Feb 13 (2012) Read article in PubMedCentral
  • Sampson J. M., Ke, W., Bethel, C. R., Pagadala, S. R. R., Nottingham, M. D., Bonomo R. A., Buynak, J. D., and van den Akker F. “Ligand dependent disorder of the omega loop observed in extended-spectrum SHV-type beta-lactamases” Antimicrob Agents Chemother 55 (1): 2303-2309 (2011). Read article in PubMedCentral
  • Ke W., Sampson J. M., Ori C., Prati F., Drawz S. M., Bethel C. R., Bonomo R. A., and 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” Antimicrob Agents Chemother 55 (1): 174-83 (2011). Read article in PubMedCentral
  • Ma X., Beuve A., and van den Akker F. “Crystal structure of the signaling helix coiled-coil domain of the beta1 subunit of the soluble guanylyl cyclase” BMC Struct Biol 10: 2 (2010). Read article in PubMedCentral
  • Martin F., Baskaran P., Ma X., Dunten P. W., Schaefer M., Stasch J. P., Beuve A., and 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” J Biol Chem 285 (29): 22651-7 (2010). Read article in PubMedCentral
  • Pattanaik P., Bethel C. R., Hujer A. M., Hujer K. M., Distler A. M., Taracila M., Anderson V. E., Fritsche T. R., Jones R. N., Pagadala S. R., van den Akker F., Buynak J. D., and Bonomo R. A. “Strategic design of an effective beta-lactamase inhibitor: LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone” J Biol Chem 284 (2): 945-53 (2009). Read article in PubMedCentral
  • Ma X., Sayed N., Baskaran P., Beuve A., and van den Akker F. “PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure” J Biol Chem 283 (2): 1167-78 (2008). Read article in PubMedCentral
  • Ma X., Sayed N., Beuve A., and van den Akker F. “NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism” EMBO J 26 (2): 578-88 (2007). Read article in PubMedCentral
  • Sayed N., Baskaran P., Ma X., van den Akker F., and Beuve A. “Desensitization of soluble guanylyl cyclase, the NO receptor, by S-nitrosylation” Proc Natl Acad Sci U S A 104 (30): 12312-7 (2007). Read article in PubMedCentral
  • Padayatti P. S., Sheri A., Totir M. A., Helfand M. S., Carey M. P., Anderson V. E., Carey P. R., Bethel C. R., Bonomo R. A., Buynak J. D., and 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” J Am Chem Soc 128 (40): 13235-42 (2006). Read article in PubMedCentral