Alsenani, T.A., Viviani, S.L., Papp-Wallace, K.M., Bonomo, R.A., van den Akker, F. (2023) “
Exploring avibactam and relebactam inhibition of Klebsiella pneumoniae carbapenemase D179N variant: role of the Ω loop-held deacylation water.
” Antimicrob Agents Chemother. 2023, e0035023. Read article in Pubmed
Kumar, V., Boorman, J., Greenlee, W.J., Zeng, X., Lin, J., van den Akker, F. (2023) “
Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter
jejuni via targeting different sites with different scaffolds."
“ Protein Sci. 2023, e4683. Read article in Pubmed
Alsenani, T.A., Rodríguez, M.M., Ghiglione, B., Taracila, M.A., Mojica, M.F., Rojas, L.J., Hujer, A.M., Gutkind, G., Bethel, C.R., Rather, P.N., Introvigne, M.L., Prati, F., Caselli, E., Power, P., van den Akker, F., Bonomo, R.A. “
Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M β-Lactamases: Biochemical and Structural Analyses.
” Antimicrob Agents Chemother. 2023, e0093022. Read article in Pubmed
Alsenani, T.A., Viviani, S.L., Kumar, V., Taracila, M.A., Bethel, C.R., Barnes, M.D., Papp-Wallace, K.M., Shields, R.K., Nguyen, M.H., Clancy, C.J., Bonomo, R.A., van den Akker, F. “
Structural characterization of the D179N and D179Y variants of KPC-2 β-lactamase: Ω loop destabilization as a mechanism of resistance to ceftazidime/avibactam.
” Antimicrob Agents Chemother. 2022, e0241421 Read article in Pubmed
Taracila, M.A., Bethel, C.R., Hujer, A.M., Papp-Wallace, K.M., Barnes, M.D., Rutter, J.D., VanPelt, J., Shurina, B.A., van den Akker, F., Clancy, C.J., Nguyen, M.H., Cheng, S., Shields, R.K., Page, R.C., and Bonomo, R.A. “
Different Conformations Revealed by Nuclear Magnetic Resonance (NMR) Underlie Resistance to Ceftazidime/Avibactam and Susceptibility to Meropenem and Imipenem among D179Y Variants of KPC -lactamase.
” Antimicrob Agents Chemother. 2022, e0212421 Read article in Pubmed
Kumar, V., Viviani, S.L., Ismail, J., Agarwal, S., Bonomo, R.A., van den Akker, F. “
Structural analysis of the boronic acid β-lactamase inhibitor vaborbactam binding to Pseudomonas aeruginosa penicillin-binding protein 3 ” PLOS ONE 2021, 16, e0258359 Read article in Pubmed
Goldberg, J., Kumar, V., Spencer, E., Hoyer, D., Marshall, S., Hujer, A., Hujer, K., Bethel, C., Papp-Wallace, K.M.,
Perez, F., Jacobs, M., van Duin, D., Kreiswirth, B., van den Akker, F.*, Plummer, M.*, Bonomo, R.A.* “
A γ-Lactam Siderophore Antibiotic Effective Against Multidrug-Resistant Pseudomonas aeruginosa , Klebsiella
pneumoniae , and Acinetobacter spp. ” Eur. J. Med. Chem. 2021, 220, 113436. Read article in Pubmed
Hahn, M.G., Lampe, T., Sheikh, S. Griebenow, N., Woltering, E., Schlemmer, K.-H., Dietz, L., Gerisch, M., Wunder, F., Becker-Pelster, E.-M.,
Modritzki, T., Tinel, H., Knorr, A., Kern, A., Lang, D., Hüser, J., Schomber, T., Benardeau, A., Eitner, F.,
Trübel, H., Mittendorf, J., Kumar, V., van den Akker, F., Schaefer, M., Geiss, V., Sandner, P., Stasch, J.-H.,
“ Discovery of the Soluble Guanylate Cyclase Activator Runcaciguat (BAY 1101042). ” J. Med. Chem. 2021, Apr 19, Online ahead of print Read article in Pubmed
Kumar, V. Mathure, S.A., 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 Campylobacter jejuni. ”
Biochemistry 2021, 60, 1133-1144 Read article in Pubmed
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 β-lactamase inhibitors and β-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 β-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 β-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 β-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 β-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. “ β-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 β-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 β-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 β-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 β-lactamase inhibition strategy probed in inhibitor-resistant SHV β-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 β-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 β-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 β-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 β1 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 β-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 β-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
Difference Density Quality (DDQ) crystal structure validation software developed by Focco van den Akker is described in this van den Akker & Hol publication. To obtain the DDQ software, please contact Dr. Focco van den Akker.