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Current Pharmaceutical Design

Editor-in-Chief

ISSN (Print): 1381-6128
ISSN (Online): 1873-4286

Mini-Review Article

Development of Peptide-based Metallo-β-lactamase Inhibitors as a New Strategy to Combat Antimicrobial Resistance: A Mini-review

Author(s): Qipeng Cheng, Ping Zeng, Edward Wai Chi Chan and Sheng Chen*

Volume 28, Issue 44, 2022

Published on: 17 October, 2022

Page: [3538 - 3545] Pages: 8

DOI: 10.2174/1381612828666220929154255

Price: $65

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Abstract

Global dissemination of antimicrobial resistance (AMR) not only poses a significant threat to human health, food security, and social development but also results in millions of deaths each year. In Gram-negative bacteria, the primary mechanism of resistance to β-lactam antibiotics is the production of β-lactamases, one of which is carbapenem-hydrolyzing β-lactamases known as carbapenemases. As a general scheme, these enzymes are divided into Ambler class A, B, C, and D based on their protein sequence homology. Class B β-lactamases are also known as metallo-β-lactamases (MBLs). The incidence of recovery of bacteria expressing metallo-β- lactamases (MBLs) has increased dramatically in recent years, almost reaching a pandemic proportion. MBLs can be further divided into three subclasses (B1, B2, and B3) based on the homology of protein sequences as well as the differences in zinc coordination. The development of inhibitors is one effective strategy to suppress the activities of MBLs and restore the activity of β-lactam antibiotics. Although thousands of MBL inhibitors have been reported, none have been approved for clinical use. This review describes the clinical application potential of peptide-based drugs that exhibit inhibitory activity against MBLs identified in past decades. In this report, peptide-based inhibitors of MBLs are divided into several groups based on the mode of action, highlighting compounds of promising properties that are suitable for further advancement. We discuss how traditional computational tools, such as in silico screening and molecular docking, along with new methods, such as deep learning and machine learning, enable a more accurate and efficient design of peptide-based inhibitors of MBLs.

Keywords: metallo-β-lactamases (MBLs), peptide-based inhibitors, in silico screening, molecular docking, deep learning, machine learning

[1]
Blair JMA, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJV. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol 2015; 13(1): 42-51.
[http://dx.doi.org/10.1038/nrmicro3380] [PMID: 25435309]
[2]
Larsson DGJ, Flach CF. Antibiotic resistance in the environment. Nat Rev Microbiol 2022; 20(5): 257-69.
[http://dx.doi.org/10.1038/s41579-021-00649-x] [PMID: 34737424]
[3]
Ramirez JA. Overview of community-acquired pneumonia in adults. Waltham, MA 2019.
[4]
Manohar P, Loh B, Nachimuthu R, Hua X, Welburn SC, Leptihn S. Secondary bacterial infections in patients with viral pneumonia. Front Med (Lausanne) 2020; 7: 420.
[http://dx.doi.org/10.3389/fmed.2020.00420] [PMID: 32850912]
[5]
Lange C, Dheda K, Chesov D, Mandalakas AM, Udwadia Z, Horsburgh CR Jr. Management of drug-resistant tuberculosis. Lancet 2019; 394(10202): 953-66.
[http://dx.doi.org/10.1016/S0140-6736(19)31882-3] [PMID: 31526739]
[6]
Goldstein E, Lipsitch M. The relation between prescribing of different antibiotics and rates of mortality with sepsis in US adults. BMC Infect Dis 2020; 20(1): 169.
[http://dx.doi.org/10.1186/s12879-020-4901-7] [PMID: 32087679]
[7]
Murray CJL, Ikuta KS, Sharara F, et al. Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. Lancet 2022; 399(10325): 629-55.
[http://dx.doi.org/10.1016/S0140-6736(21)02724-0] [PMID: 35065702]
[8]
Breijyeh Z, Jubeh B, Karaman R. Resistance of gram-negative bacteria to current antibacterial agents and approaches to resolve it. Molecules 2020; 25(6): 1340.
[http://dx.doi.org/10.3390/molecules25061340] [PMID: 32187986]
[9]
Doi Y, Bonomo RA, Hooper DC, et al. Gram-negative bacterial infections: Research priorities, accomplishments, and future directions of the antibacterial resistance leadership group. Clin Infect Dis 2017; 64 (Suppl. 1): S30-5.
[http://dx.doi.org/10.1093/cid/ciw829] [PMID: 28350901]
[10]
Munita JM, Arias CA. Mechanisms of antibiotic resistance. In: Indira TK, Nancy AC, Paul JP, et al., Eds., Virulence Mechanisms of Bacterial Pathogens. (5th Edition.). 2016; pp. 481-511.
[http://dx.doi.org/10.1128/9781555819286.ch17]
[11]
King DT, Sobhanifar S, Strynadka NC, Gotte M. The mechanisms of resistance to b-lactam antibiotics. In: Handbook of Antimicrobial Resistance. New York: Springer 2017.
[12]
Bush K. Overcoming β-lactam resistance in gram-negative pathogens. Future Med Chem 2016; 8(9): 921-4.
[http://dx.doi.org/10.4155/fmc-2016-0076] [PMID: 27228233]
[13]
Bush K. Past and present perspectives on β-lactamases. Antimicrob Agents Chemother 2018; 62(10): e01076-18.
[http://dx.doi.org/10.1128/AAC.01076-18] [PMID: 30061284]
[14]
Ambler RP. The structure of β-lactamases. Philos Trans R Soc Lond B Biol Sci 1980; 289(1036): 321-31.
[http://dx.doi.org/10.1098/rstb.1980.0049] [PMID: 6109327]
[15]
Ambler RP, Meadway RJ. Chemical structure of bacterial penicillinases. Nature 1969; 222(5188): 24-6.
[http://dx.doi.org/10.1038/222024a0] [PMID: 4975648]
[16]
Hall BG, Barlow M. Evolution of the serine β-lactamases: Past, present and future. Drug Resist Updat 2004; 7(2): 111-23.
[http://dx.doi.org/10.1016/j.drup.2004.02.003] [PMID: 15158767]
[17]
Salahuddin P, Kumar A, Khan AU. Structure, function of serine and metallo-β-lactamases and their inhibitors. Curr Protein Pept Sci 2018; 19(2): 130-44.
[PMID: 28745223]
[18]
Palzkill T. Metallo-β-lactamase structure and function. Ann N Y Acad Sci 2013; 1277(1): 91-104.
[http://dx.doi.org/10.1111/j.1749-6632.2012.06796.x] [PMID: 23163348]
[19]
Watanabe M, Iyobe S, Inoue M, Mitsuhashi S. Transferable imipenem resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 1991; 35(1): 147-51.
[http://dx.doi.org/10.1128/AAC.35.1.147] [PMID: 1901695]
[20]
Lauretti L, Riccio ML, Mazzariol A, et al. Cloning and characterization of blaVIM, a new integron-borne metallo-beta-lactamase gene from a Pseudomonas aeruginosa clinical isolate. Antimicrob Agents Chemother 1999; 43(7): 1584-90.
[http://dx.doi.org/10.1128/AAC.43.7.1584] [PMID: 10390207]
[21]
Yong D, Toleman MA, Giske CG, et al. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 2009; 53(12): 5046-54.
[http://dx.doi.org/10.1128/AAC.00774-09] [PMID: 19770275]
[22]
Boyd SE, Livermore DM, Hooper DC, Hope WW. Metallo-β-lactamases: Structure, function, epidemiology, treatment options, and the development pipeline. Antimicrob Agents Chemother 2020; 64(10): e00397-20.
[http://dx.doi.org/10.1128/AAC.00397-20] [PMID: 32690645]
[23]
Han R, Shi Q, Wu S, et al. Dissemination of carbapenemases (KPC, NDM, OXA-48, IMP, and VIM) among carbapenemresistant Enterobacteriaceae isolated from adult and children patients in China. Front Cell Infect Microbiol 2020; 10: 314.
[http://dx.doi.org/10.3389/fcimb.2020.00314] [PMID: 32719751]
[24]
Bush K, Bradford PA. Interplay between β-lactamases and new β-lactamase inhibitors. Nat Rev Microbiol 2019; 17(5): 295-306.
[http://dx.doi.org/10.1038/s41579-019-0159-8] [PMID: 30837684]
[25]
Drawz SM, Bonomo RA. Three decades of β-lactamase inhibitors. Clin Microbiol Rev 2010; 23(1): 160-201.
[http://dx.doi.org/10.1128/CMR.00037-09] [PMID: 20065329]
[26]
Ehmann DE, Jahić H, Ross PL, et al. Kinetics of avibactam inhibition against class A, C, and D β-lactamases. J Biol Chem 2013; 288(39): 27960-71.
[http://dx.doi.org/10.1074/jbc.M113.485979] [PMID: 23913691]
[27]
Hirsch EB, Ledesma KR, Chang KT, Schwartz MS, Motyl MR, Tam VH. In vitro activity of MK-7655, a novel β-lactamase inhibitor, in combination with imipenem against carbapenem-resistant Gram-negative bacteria. Antimicrob Agents Chemother 2012; 56(7): 3753-7.
[http://dx.doi.org/10.1128/AAC.05927-11] [PMID: 22526311]
[28]
Hecker SJ, Reddy KR, Totrov M, et al. Discovery of a cyclic boronic acid β-lactamase inhibitor (RPX7009) with utility vs. class A serine carbapenemases. J Med Chem 2015; 58(9): 3682-92.
[http://dx.doi.org/10.1021/acs.jmedchem.5b00127] [PMID: 25782055]
[29]
Papp-Wallace KM, Barnes MD, Alsop J, et al. Relebactam is a potent inhibitor of the KPC-2 β-lactamase and restores imipenem susceptibility in KPC-producing Enterobacteriaceae. Antimicrob Agents Chemother 2018; 62(6): e00174-18.
[http://dx.doi.org/10.1128/AAC.00174-18] [PMID: 29610205]
[30]
Stachyra T, Levasseur P, Péchereau MC, et al. In vitro activity of the -lactamase inhibitor NXL104 against KPC-2 carbapenemase and Enterobacteriaceae expressing KPC carbapenemases. J Antimicrob Chemother 2009; 64(2): 326-9.
[http://dx.doi.org/10.1093/jac/dkp197] [PMID: 19493866]
[31]
Lomovskaya O, Sun D, Rubio-Aparicio D, et al. Vaborbactam: Spectrum of beta-lactamase inhibition and impact of resistance mechanisms on activity in Enterobacteriaceae. Antimicrob Agents Chemother 2017; 61(11): e01443-17.
[http://dx.doi.org/10.1128/AAC.01443-17] [PMID: 28848018]
[32]
Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the age of multidrug resistance: From structure and mechanism to evolution, dissemination, and inhibitor design. Chem Rev 2021; 121(13): 7957-8094.
[http://dx.doi.org/10.1021/acs.chemrev.1c00138] [PMID: 34129337]
[33]
Muttenthaler M, King GF, Adams DJ, Alewood PF. Trends in peptide drug discovery. Nat Rev Drug Discov 2021; 20(4): 309-25.
[http://dx.doi.org/10.1038/s41573-020-00135-8] [PMID: 33536635]
[34]
Wang L, Wang N, Zhang W, et al. Therapeutic peptides: Current applications and future directions. Signal Transduct Target Ther 2022; 7(1): 48.
[http://dx.doi.org/10.1038/s41392-022-00904-4] [PMID: 35165272]
[35]
Henninot A, Collins JC, Nuss JM. The current state of peptide drug discovery: Back to the future? J Med Chem 2018; 61(4): 1382-414.
[http://dx.doi.org/10.1021/acs.jmedchem.7b00318] [PMID: 28737935]
[36]
Magana M, Pushpanathan M, Santos AL, et al. The value of antimicrobial peptides in the age of resistance. Lancet Infect Dis 2020; 20(9): e216-30.
[http://dx.doi.org/10.1016/S1473-3099(20)30327-3] [PMID: 32653070]
[37]
Zeng P, Xu C, Cheng Q, et al. Phenol‐soluble‐modulin‐inspired amphipathic peptides have bactericidal activity against multidrug‐resistant bacteria. ChemMedChem 2019; 14(16): 1547-59.
[http://dx.doi.org/10.1002/cmdc.201900364] [PMID: 31359624]
[38]
Zhang L, Gallo RL. Antimicrobial peptides. Curr Biol 2016; 26(1): R14-9.
[http://dx.doi.org/10.1016/j.cub.2015.11.017] [PMID: 26766224]
[39]
Naas T, Oueslati S, Bonnin RA, et al. Beta-lactamase database (BLDB) – structure and function. J Enzyme Inhib Med Chem 2017; 32(1): 917-9.
[http://dx.doi.org/10.1080/14756366.2017.1344235] [PMID: 28719998]
[40]
Schnaars C, Kildahl-Andersen G, Prandina A, et al. Synthesis and preclinical evaluation of TPA-based zinc chelators as metallo-β-lactamase inhibitors. ACS Infect Dis 2018; 4(9): 1407-22.
[http://dx.doi.org/10.1021/acsinfecdis.8b00137] [PMID: 30022668]
[41]
Kildahl-Andersen G, Schnaars C, Prandina A, et al. Synthesis and biological evaluation of zinc chelating compounds as metallo-β-lactamase inhibitors. MedChemComm 2019; 10(4): 528-37.
[http://dx.doi.org/10.1039/C8MD00578H] [PMID: 31057732]
[42]
Pace N, Weerapana E. Zinc-binding cysteines: Diverse functions and structural motifs. Biomolecules 2014; 4(2): 419-34.
[http://dx.doi.org/10.3390/biom4020419] [PMID: 24970223]
[43]
Bounaga S, Galleni M, Laws AP, Page MI. Cysteinyl peptide inhibitors of Bacillus cereus zinc β-lactamase. Bioorg Med Chem 2001; 9(2): 503-10.
[http://dx.doi.org/10.1016/S0968-0896(00)00257-1] [PMID: 11249142]
[44]
Sun Q, Law A, Crowder MW, Geysen HM. Homo-cysteinyl peptide inhibitors of the L1 metallo-β-lactamase, and SAR as determined by combinatorial library synthesis. Bioorg Med Chem Lett 2006; 16(19): 5169-75.
[http://dx.doi.org/10.1016/j.bmcl.2006.07.001] [PMID: 16875814]
[45]
Shen B, Zhu C, Gao X, Liu G, Song J, Yu Y. Oligopeptides as full-length New Delhi metallo-β-lactamase-1 (NDM-1) inhibitors. PLoS One 2017; 12(5): e0177293.
[http://dx.doi.org/10.1371/journal.pone.0177293] [PMID: 28542279]
[46]
Fehlbaum P, Bulet P, Chernysh S, et al. Structure-activity analysis of thanatin, a 21-residue inducible insect defense peptide with sequence homology to frog skin antimicrobial peptides. Proc Natl Acad Sci USA 1996; 93(3): 1221-5.
[http://dx.doi.org/10.1073/pnas.93.3.1221] [PMID: 8577744]
[47]
Ma B, Fang C, Lu L, et al. The antimicrobial peptide thanatin disrupts the bacterial outer membrane and inactivates the NDM-1 metallo-β-lactamase. Nat Commun 2019; 10(1): 3517.
[http://dx.doi.org/10.1038/s41467-019-11503-3] [PMID: 31388008]
[48]
Moura ECCM, Baeta T, Romanelli A, et al. Thanatin impairs lipopolysaccharide transport complex assembly by targeting LptC–LptA interaction and decreasing LptA stability. Front Microbiol 2020; 11: 909.
[http://dx.doi.org/10.3389/fmicb.2020.00909] [PMID: 32477309]
[49]
Selvaraju G, Leow TC, Salleh AB, Normi YM. Design and characterisation of inhibitory peptides against Bleg1_2478, an evolutionary divergent B3 metallo-β-lactamase. Molecules 2020; 25(24): 5797.
[http://dx.doi.org/10.3390/molecules25245797] [PMID: 33316879]
[50]
Mulligan VK, Workman S, Sun T, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. PNAS 2021; 118(12): e2012800118.
[http://dx.doi.org/10.1073/pnas.2012800118]
[51]
Bhardwaj G, Mulligan VK, Bahl CD, et al. Accurate de novo design of hyperstable constrained peptides. Nature 2016; 538(7625): 329-35.
[http://dx.doi.org/10.1038/nature19791] [PMID: 27626386]
[52]
Hosseinzadeh P, Bhardwaj G, Mulligan VK, et al. Comprehensive computational design of ordered peptide macrocycles. Science 2017; 358(6369): 1461-6.
[http://dx.doi.org/10.1126/science.aap7577] [PMID: 29242347]
[53]
Rotondo CM, Marrone L, Goodfellow VJ, et al. Arginine-containing peptides as potent inhibitors of VIM-2 metallo-β-lactamase. Biochim Biophys Acta, Gen Subj 2015; 1850(11): 2228-38.
[http://dx.doi.org/10.1016/j.bbagen.2015.07.012] [PMID: 26238337]
[54]
Sohier JS, Laurent C, Chevigné A, et al. Allosteric inhibition of VIM metallo-β-lactamases by a camelid nanobody. Biochem J 2013; 450(3): 477-86.
[http://dx.doi.org/10.1042/BJ20121305] [PMID: 23289540]
[55]
Conrath KE, Lauwereys M, Galleni M, et al. β-lactamase inhibitors derived from single-domain antibody fragments elicited in the camelidae. Antimicrob Agents Chemother 2001; 45(10): 2807-12.
[http://dx.doi.org/10.1128/AAC.45.10.2807-2812.2001] [PMID: 11557473]
[56]
Ben Abderrazek R, Chammam S, Ksouri A, et al. Inhibitory potential of polyclonal camel antibodies against new delhi metallo-β-lactamase-1 (NDM-1). Molecules 2020; 25(19): 4453.
[http://dx.doi.org/10.3390/molecules25194453] [PMID: 32998307]
[57]
Sully EK, Geller BL, Li L, et al. Peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) restores carbapenem susceptibility to NDM-1-positive pathogens in vitro and in vivo. J Antimicrob Chemother 2017; 72(3): 782-90.
[PMID: 27999041]
[58]
Mellbye BL, Puckett SE, Tilley LD, Iversen PL, Geller BL. Variations in amino acid composition of antisense peptide-phosphorodiamidate morpholino oligomer affect potency against Escherichia coli in vitro and in vivo. Antimicrob Agents Chemother 2009; 53(2): 525-30.
[http://dx.doi.org/10.1128/AAC.00917-08] [PMID: 19015356]
[59]
Greenberg DE, Marshall-Batty KR, Brinster LR, et al. Antisense phosphorodiamidate morpholino oligomers targeted to an essential gene inhibit Burkholderia cepacia complex. J Infect Dis 2010; 201(12): 1822-30.
[http://dx.doi.org/10.1086/652807] [PMID: 20438352]
[60]
Readman JB, Dickson G, Coldham NG. Translational inhibition of CTX-M extended spectrum β-lactamase in clinical strains of Escherichia coli by synthetic antisense oligonucleotides partially restores sensitivity to cefotaxime. Front Microbiol 2016; 7: 373.
[http://dx.doi.org/10.3389/fmicb.2016.00373] [PMID: 27047482]
[61]
Wang X, Wang Y, Ling Z, et al. Peptide nucleic acid restores colistin susceptibility through modulation of MCR-1 expression in Escherichia coli. J Antimicrob Chemother 2020; 75(8): dkaa140.
[http://dx.doi.org/10.1093/jac/dkaa140] [PMID: 32417908]
[62]
Daly SM, Sturge CR, Felder-Scott CF, Geller BL, Greenberg DE. MCR-1 inhibition with peptide-conjugated phosphorodiamidate morpholino oligomers restores sensitivity to polymyxin in Escherichia coli. MBio 2017; 8(6): e01315-7.
[http://dx.doi.org/10.1128/mBio.01315-17] [PMID: 29114023]
[63]
Kazi MI, Perry BW, Card DC, et al. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 2020; 75(10): 2843-51.
[http://dx.doi.org/10.1093/jac/dkaa242] [PMID: 32591801]
[64]
Somboro AM, Osei Sekyere J, Amoako DG, Essack SY, Bester LA. Diversity and proliferation of metallo-β-lactamases: A clarion call for clinically effective metallo-β-lactamase inhibitors. Appl Environ Microbiol 2018; 84(18): e00698-18.
[http://dx.doi.org/10.1128/AEM.00698-18] [PMID: 30006399]
[65]
Mojica MF, Rossi M-A, Vila AJ, Bonomo RA. The urgent need for metallo-β-lactamase inhibitors: An unattended global threat. Lancet Infect Dis 2021.
[PMID: 34246322]
[66]
Montagner C, Nigen M, Jacquin O, et al. The role of active site flexible loops in catalysis and of zinc in conformational stability of Bacillus cereus 569/H/9 β-lactamase. J Biol Chem 2016; 291(31): 16124-37.
[http://dx.doi.org/10.1074/jbc.M116.719005] [PMID: 27235401]
[67]
Brem J, Struwe WB, Rydzik AM, et al. Studying the active-site loop movement of the São Paolo metallo-β-lactamase-1. Chem Sci (Camb) 2015; 6(2): 956-63.
[http://dx.doi.org/10.1039/C4SC01752H]
[68]
Zhang H, Ma G, Zhu Y, et al. Active-site conformational fluctuations promote the enzymatic activity of NDM-1. Antimicrob Agents Chemother 2018; 62(11): e01579-18.
[http://dx.doi.org/10.1128/AAC.01579-18] [PMID: 30150473]
[69]
de Ruyck J, Brysbaert G, Blossey R, Lensink M. Molecular docking as a popular tool in drug design, an in silico travel. Adv Appl Bioinform Chem 2016; 9: 1-11.
[http://dx.doi.org/10.2147/AABC.S105289] [PMID: 27390530]
[70]
Haga JH, Ichikawa K, Date S, Ichikawa K. Virtual screening techniques and current computational infrastructures. Curr Pharm Des 2016; 22(23): 3576-84.
[http://dx.doi.org/10.2174/1381612822666160414142530] [PMID: 27075580]
[71]
Seifert MHJ, Wolf K, Vitt D. Virtual high-throughput in silico screening. BIOSILICO 2003; 1(4): 143-9.
[http://dx.doi.org/10.1016/S1478-5382(03)02359-X]
[72]
Capecchi A, Cai X, Personne H, Köhler T, van Delden C, Reymond JL. Machine learning designs non-hemolytic antimicrobial peptides. Chem Sci (Camb) 2021; 12(26): 9221-32.
[http://dx.doi.org/10.1039/D1SC01713F] [PMID: 34349895]
[73]
Wang C, Garlick S, Zloh M. Deep learning for novel antimicrobial peptide design. Biomolecules 2021; 11(3): 471.
[http://dx.doi.org/10.3390/biom11030471] [PMID: 33810011]
[74]
Plisson F, Ramírez-Sánchez O, Martínez-Hernández C. Machine learning-guided discovery and design of non-hemolytic peptides. Sci Rep 2020; 10(1): 16581.
[http://dx.doi.org/10.1038/s41598-020-73644-6] [PMID: 33024236]
[75]
Charoenkwan P, Anuwongcharoen N, Nantasenamat C, Hasan MM, Shoombuatong W. In silico approaches for the prediction and analysis of antiviral peptides: A review. Curr Pharm Des 2021; 27(18): 2180-8.
[http://dx.doi.org/10.2174/1381612826666201102105827] [PMID: 33138759]

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