Abstract
Proteases are enzymes that catalyze the amide bond dissociation in polypeptide and protein peptide units. They are categorized into seven families and are responsible for a wide spectrum of human ailments, such as various types of cancers, skin infections, urinary tract infections etc. Specifically, the bacterial proteases cause a huge impact in the disease progression. Extracellular bacterial proteases break down the host defense proteins, while intracellular proteases are essential for pathogens virulence. Due to its involvement in disease pathogenesis and virulence, bacterial proteases are considered to be potential drug targets. Several studies have reported potential bacterial protease inhibitors in both Gram-positive and Gram-negative disease causing pathogens. In this study, we have comprehensively reviewed about the various human disease-causing cysteine, metallo, and serine bacterial proteases as well as their potential inhibitors.
Similar content being viewed by others
Data availability
All the data that is used for preparing this manuscript is provided.
References
Basha S, Rai P, Poon V, Saraph A, Gujraty K, Go MY, Sadacharan S, Frost M, Mogridge J, Kane RS (2006) Polyvalent inhibitors of anthrax toxin that target host receptors. Proc Natl Acad Sci 103(36):13509–13513
Berggren K, Johansson B, Fex T, Kihlberg J, Björck L, Luthman K (2009) Synthesis and biological evaluation of reversible inhibitors of IdeS, a bacterial cysteine protease and virulence determinant. Bioorg Med Chem 17(9):3463–3470
Berggren K, Vindebro R, Bergström C, Spoerry C, Persson H, Fex T, Kihlberg J, von Pawel-Rammingen U, Luthman K (2012) 3-Aminopiperidine-based peptide analogues as the first selective noncovalent inhibitors of the bacterial cysteine protease Ides. J Med Chem 55(6):2549–2560
Bhandari V, Wong KS, Zhou JL, Mabanglo MF, Batey RA, Houry WA (2018) The role of ClpP protease in bacterial pathogenesis and human diseases. ACS Chem Biol 13(6):1413–1425
Bhattacharya AK, Rana KC, Raut DS, Mhaindarkar VP, Khan MI (2011) An efficient synthesis of benzodiazepinyl phosphonates as clostripain inhibitors via FeCl3 catalyzed four-component reaction. Org Biomol Chem 9(15):5407–5413
Boleij A, Hechenbleikner EM, Goodwin AC, Badani R, Stein EM, Lazarev MG, Ellis B, Carroll KC, Albesiano E, Wick EC, Platz EA (2015) The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients. Clin Infect Dis 60(2):208–215
Bussiere DE, Pratt SD, Katz L, Severin JM, Holzman T, Park CH (1998) The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol Cell 2(1):75–84
Cassenego AP, de Oliveira NE, Laport MS, Abranches J, Lemos JA, Giambiagi-deMarval M (2016) The CtsR regulator controls the expression of clpC, clpE and clpP and is required for the virulence of Enterococcus faecalis in an invertebrate model. Antonie Van Leeuwenhoek 109(9):1253–1259
Chakravorty A, Awad MM, Hiscox TJ, Cheung JK, Carter GP, Choo JM, Lyras D, Rood JI (2011) The cysteine protease α-Clostripain is not essential for the pathogenesis of Clostridium perfringens-mediated Myonecrosis. PLoS ONE 6(7):e22762
Choules MP, Wolf NM, Lee H, Anderson JR, Grzelak EM, Wang Y, Ma R, Gao W, McAlpine JB, Jin YY, Cheng J (2019) Rufomycin targets ClpC1 proteolysis in Mycobacterium tuberculosis and M. abscessus. Antimicrobial Agents Chemother 63(3):e02204-e2218
Culp E, Wright GD (2017) Bacterial proteases, untapped antimicrobial drug targets. J Antibiot 70(4):366–377
Dominy SS, Lynch C, Ermini F, Benedyk M, Marczyk A, Konradi A, Nguyen M, Haditsch U, Raha D, Griffin C, Holsinger LJ (2019) Porphyromonas gingivalis in Alzheimer’s disease brains: evidence for disease causation and treatment with small-molecule inhibitors. Sci Adv 5(1):eaau3333
Famulla K, Sass P, Malik I, Akopian T, Kandror O, Alber M, Hinzen B, Ruebsamen-Schaeff H, Kalscheuer R, Goldberg AL, Brötz-Oesterhelt H (2016) Acyldepsipeptide antibiotics kill mycobacteria by preventing the physiological functions of the ClpP1P2 protease. Mol Microbiol 101(2):194–209
Filipek R, Rzychon M, Oleksy A, Gruca M, Dubin A, Potempa J, Bochtler M (2003) The staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease. J Biol Chem 278(42):40959–40966
Fitzpatrick RE, Wijeyewickrema LC, Pike RN (2009) The gingipains: scissors and glue of the periodontal pathogen Porphyromonas Gingivalis. Fut Microbiol 4:471–487. https://doi.org/10.2217/fmb.09.18
Gaillot O, Pellegrini E, Bregenholt S, Nair S, Berche P (2000) The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes. Mol Microbiol 35(6):1286–1294
Gao W, Kim JY, Anderson JR, Akopian T, Hong S, Jin YY, Kandror O, Kim JW, Lee IA, Lee SY, McAlpine JB (2015) The cyclic peptide ecumicin targeting ClpC1 is active against Mycobacterium tuberculosis in vivo. Antimicrob Agents Chemother 59(2):880–889
Gavrish E, Sit CS, Cao S, Kandror O, Spoering A, Peoples A, Ling L, Fetterman A, Hughes D, Bissell A, Torrey H (2014) Lassomycin, a ribosomally synthesized cyclic peptide, kills Mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem Biol 21(4):509–518
Gilles AM, Imhoff JM, Keil B (1979) Alpha-Clostripain—Chemical characterization, activity, and thiol content of the highly active form of clostripain. J Biol Chem 254(5):1462–1468
Goldberg AB, Turk BE (2016) Inhibitors of the metalloproteinase anthrax lethal factor. Curr Top Med Chem 16(21):2350–2358
Goulas T, Arolas JL, Gomis-Rüth FX (2011) Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog. Proc Natl Acad Sci 108(5):1856–1861
Gusman H, Grogan J, Kagan HM, Troxler RF, Oppenheim FG (2001) Salivary histatin 5 is a potent competitive inhibitor of the cysteine proteinase clostripain. FEBS Lett 489(1):97–100
Kagawa TF, O’toole PW, Cooney JC (2005) SpeB–spi: a novel protease–inhibitor pair from Streptococcus pyogenes. Mol Microbiol 57(3):650–666
Kalińska M, Kantyka T, Greenbaum DC, Larsen KS, Władyka B, Jabaiah A, Bogyo M, Daugherty PS, Wysocka M, Jaros M, Lesner A (2012) Substrate specificity of Staphylococcus aureus cysteine proteases–Staphopains A, B and C. Biochimie 94(2):318–327
Kataoka S, Baba A, Suda Y, Takii R, Hashimoto M, Kawakubo T, Asao T, Kadowaki T, Yamamoto K (2014) A novel, potent dual inhibitor of Arg-gingipains and Lys-gingipain as a promising agent for periodontal disease therapy. FASEB J 28(8):3564–3578
Kembhavi AA, Buttle DJ, Rauber P, Barrett AJ (1991) Clostripain: characterization of the active site. FEBS Lett 283(2):277–280
Kim HS, Kim J, Im HN, An DR, Lee M, Hesek D, Mobashery S, Kim JY, Cho K, Yoon HJ, Han BW (2014) Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, ad, l-carboxypeptidase controlling the helical cell shape. Acta Crystallogr D Biol Crystallogr 70(11):2800–2812
Knudsen GM, Olsen JE, Aabo S, Barrow P, Rychlik I, Thomsen LE (2013) ClpP deletion causes attenuation of Salmonella Typhimurium virulence through mis-regulation of RpoS and indirect control of CsrA and the SPI genes. Microbiology 159(Pt_7):1497–1509
Kulig P, Zabel BA, Dubin G, Allen SJ, Ohyama T, Potempa J, Handel TM, Butcher EC, Cichy J (2007) Staphylococcus aureus-derived staphopain B, a potent cysteine protease activator of plasma chemerin. J Immunol 178(6):3713–3720
Kusters JG, Van Vliet AH, Kuipers EJ (2006) Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev 19(3):449–490
Kwon HY, Ogunniyi AD, Choi MH, Pyo SN, Rhee DK, Paton JC (2004) The ClpP protease of Streptococcus pneumoniae modulates virulence gene expression and protects against fatal pneumococcal challenge. Infect Immun 72(10):5646–5653
Laarman AJ, Mijnheer G, Mootz JM, Van Rooijen WJ, Ruyken M, Malone CL, Heezius EC, Ward R, Milligan G, Van Strijp JA, De Haas CJ (2012) Staphylococcus aureus Staphopain A inhibits CXCR2-dependent neutrophil activation and chemotaxis. EMBO J 31(17):3607–3619
Lane MD, Seelig B (2016) Highly efficient recombinant production and purification of streptococcal cysteine protease streptopain with increased enzymatic activity. Protein Expr Purif 121:66–72
Lessard IA, Walsh CT (1999) VanX, a bacterial D-alanyl-D-alanine dipeptidase: resistance, immunity, or survival function? Proc Natl Acad Sci 96(20):11028–11032
Leung E, Datti A, Cossette M, Goodreid J, McCaw SE, Mah M, Nakhamchik A, Ogata K, El Bakkouri M, Cheng YQ, Wodak SJ (2011) Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease. Chem Biol 18(9):1167–1178
Lipinska BA, Fayet O, Baird L, Georgopoulos CO (1989) Identification, characterization, and mapping of the Escherichia coli htrA gene, whose product is essential for bacterial growth only at elevated temperatures. J Bacteriol 171(3):1574–1584
Liu Y, Zhang Y, Wang L, Guo Y, Xiao S (2013) Prevalence of Porphyromonas gingivalis four rag locus genotypes in patients of orthodontic gingivitis and periodontitis. PLoS ONE 8(4):e61028
Liu Y, Frirdich E, Taylor JA, Chan AC, Blair KM, Vermeulen J, Ha R, Murphy ME, Salama NR, Gaynor EC, Tanner ME (2016) A bacterial cell shape-determining inhibitor. ACS Chem Biol 11(4):981–991
Lourbakos A, Potempa J, Travis J, D’Andrea MR, Andrade-Gordon P, Santulli R, Mackie EJ, Pike RN (2001) Arginine-specific protease from Porphyromonas gingivalis activates protease-activated receptors on human oral epithelial cells and induces interleukin-6 secretion. Infect Immun 69(8):5121–5130
Löwer M, Geppert T, Schneider P, Hoy B, Wessler S, Schneider G (2011) Inhibitors of Helicobacter pylori protease HtrA found by ‘virtual ligand’screening combat bacterial invasion of epithelia. PLoS ONE 6(3):e17986
Mei JM, Nourbakhsh F, Ford CW, Holden DW (1997) Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis. Mol Microbiol 26(2):399–407
Metz P, Tjan MJ, Wu S, Pervaiz M, Hermans S, Shettigar A, Sears CL, Ritschel T, Dutilh BE, Boleij A (2019) Drug discovery and repurposing inhibits a major gut pathogen-derived oncogenic toxin. Front Cell Infect Microbiol 9:364
Migone TS, Subramanian GM, Zhong J, Healey LM, Corey A, Devalaraja M, Lo L, Ullrich S, Zimmerman J, Chen A, Lewis M (2009) Raxibacumab for the treatment of inhalational anthrax. N Engl J Med 361(2):135–144
Mitchell WM (1977) Cleavage at arginine residues by clostripain. Methods in enzymology, vol 47. Academic Press, Cambridge, pp 165–170
Miyashita H, Honda T, Maekawa T, Takahashi N, Aoki Y, Nakajima T, Tabeta K, Yamazaki K (2012) Relationship between serum antibody titres to Porphyromonas gingivalis and hs-CRP levels as inflammatory markers of periodontitis. Arch Oral Biol 57(6):820–829
Moayeri M, Crown D, Jiao GS, Kim S, Johnson A, Leysath C, Leppla SH (2013) Small-molecule inhibitors of lethal factor protease activity protect against anthrax infection. Antimicrob Agents Chemother 57(9):4139–4145
Moreno-Cinos C, Goossens K, Salado IG, Van Der Veken P, De Winter H, Augustyns K (2019) ClpP protease, a promising antimicrobial target. Int J Mol Sci 20(9):2232
Mundra S, Thakur V, Bello AM, Rathore S, Asad M, Wei L, Yang J, Chakka SK, Mahesh R, Malhotra P, Mohmmed A (2017) A novel class of Plasmodial ClpP protease inhibitors as potential antimalarial agents. Bioorg Med Chem 25(20):5662–5677
Muthyala R, Rastogi N, Shin WS, Peterson ML, Sham YY (2014) Cell permeable vanX inhibitors as vancomycin re-sensitizing agents. Bioorg Med Chem Lett 24(11):2535–2538
Nakayama M, Inoue T, Naito M, Nakayama K, Ohara N (2015) Attenuation of the phosphatidylinositol 3-kinase/Akt signaling pathway by Porphyromonas gingivalis gingipains RgpA, RgpB, and Kgp. J Biol Chem 290(8):5190–5202
Nunes JM, Fillis T, Page MJ, Venter C, Lancry O, Kell DB, Windberger U, Pretorius E (2020) Gingipain R1 and lipopolysaccharide from Porphyromonas gingivalis have major effects on blood clot morphology and mechanics. Front Immunol 11:1551
Obiso RJ Jr, Azghani AO, Wilkins TD (1997) The Bacteroides fragilis toxin fragilysin disrupts the paracellular barrier of epithelial cells. Infect Immun 65(4):1431–1439
Pannifer AD, Wong TY, Schwarzenbacher R, Renatus M, Petosa C, Bienkowska J, Lacy DB, Collier RJ, Park S, Leppla SH, Hanna P (2001) Crystal structure of the anthrax lethal factor. Nature 414(6860):229–233
Perna AM, Reisen F, Schmidt TP, Geppert T, Pillong M, Weisel M, Hoy B, Simister PC, Feller SM, Wessler S, Schneider G (2014) Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site. Chem Sci 5(9):3583–3590
Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G (2015) Fragment-based de novo design reveals a small-molecule inhibitor of Helicobacter pylori HtrA. Angew Chem 127(35):10382–10386
Qiu D, Eisinger VM, Head NE, Pier GB, Yu HD (2008) ClpXP proteases positively regulate alginate overexpression and mucoid conversion in Pseudomonas aeruginosa. Microbiology (reading, England) 154(Pt 7):2119
Raha D, Broce S, Haditsch U, Rodriguez L, Ermini F, Detke M, Kapur S, Hennings D, Roth T, Nguyen M, Holsinger LJ (2020) COR388, a novel gingipain inhibitor, decreases fragmentation of APOE in the central nervous system of Alzheimer’s disease patients: human/human trials: other. Alzheimers Dement 16:e040578
Rai N, Muthukumaran R, Amutha R (2018) Identification of inhibitor against H. pylori HtrA protease using structure-based virtual screening and molecular dynamics simulations approaches. Microb Pathog 118:365–377
Raju RM, Unnikrishnan M, Rubin DH, Krishnamoorthy V, Kandror O, Akopian TN, Goldberg AL, Rubin EJ (2012) Mycobacterium tuberculosis ClpP1 and ClpP2 function together in protein degradation and are required for viability in vitro and during infection. PLoS Pathog 8(2):e1002511
Rathore S, Sinha D, Asad M, Böttcher T, Afrin F, Chauhan VS, Gupta D, Sieber SA, Mohmmed A (2010) A cyanobacterial serine protease of Plasmodium falciparum is targeted to the apicoplast and plays an important role in its growth and development. Mol Microbiol 77(4):873–890
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD (2018) The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res 46(D1):D624–D632
Roncase EJ, Moon C, Chatterjee S, González-Páez GE, Craik CS, O’Donoghue AJ, Wolan DW (2017) Substrate profiling and high resolution co-complex crystal structure of a secreted C11 protease conserved across commensal bacteria. ACS Chem Biol 12(6):1556–1565
Schmitt EK, Riwanto M, Sambandamurthy V, Roggo S, Miault C, Zwingelstein C, Krastel P, Noble C, Beer D, Rao SP, Au M (2011) The natural product cyclomarin kills Mycobacterium tuberculosis by targeting the ClpC1 subunit of the caseinolytic protease. Angew Chem 123(26):6011–6013
Shoop WL, Xiong Y, Wiltsie J, Woods A, Guo J, Pivnichny JV, Felcetto T, Michael BF, Bansal A, Cummings RT, Cunningham BR (2005) Anthrax lethal factor inhibition. Proc Natl Acad Sci 102(22):7958–7963
Skorko-Glonek J, Zurawa-Janicka D, Koper T, Jarzab M, Figaj D, Glaza P, Lipinska B (2013) HtrA protease family as therapeutic targets. Curr Pharm Des 19(6):977–1009
Song Y, Ke Y, Kang M, Bao R (2022) Function, molecular mechanisms, and therapeutic potential of bacterial HtrA proteins: an evolving view. Comput Struct Biotechnol J 20:40–49
Stelzner K, Boyny A, Hertlein T, Sroka A, Moldovan A, Paprotka K, Kessie D, Mehling H, Potempa J, Ohlsen K, Fraunholz MJ (2021) Intracellular Staphylococcus aureus employs the cysteine protease staphopain A to induce host cell death in epithelial cells. PLoS Pathog 17(9):e1009874
Ulger Toprak N, Yagci AY, Gulluoglu BM, Akin ML, Demirkalem P, Celenk T, Soyletir G (2006) A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. Clin Microbiol Infect 12(8):782–786
Van Amsterdam K, Van Vliet AH, Kusters JG, Van Der Ende A (2006) Of microbe and man: determinants of Helicobacter pylori-related diseases. FEMS Microbiol Rev 30(1):131–156
Veltri CA (2015) Proteases: nature’s destroyers and the drugs that stop them. Pharm Pharmacol Int J 2(6):1–1
von Pawel-Rammingen U, Johansson BP, Björck L (2002) IdeS, a novel streptococcal cysteine proteinase with unique specificity for immunoglobulin G. EMBO J 21(7):1607–1615
Wang AY, González-Páez GE, Wolan DW (2015) Identification and co-complex structure of a new S. pyogenes SpeB small molecule inhibitor. Biochemistry 54(28):4365–4373
Wessler S, Schneider G, Backert S (2017) Bacterial serine protease HtrA as a promising new target for antimicrobial therapy? Cell Commun Signal 15(1):1–5
Woehl JL, Kitamura S, Dillon N, Han Z, Edgar LJ, Nizet V, Wolan DW (2020) An irreversible inhibitor to probe the role of Streptococcus pyogenes cysteine protease SpeB in evasion of host complement defenses. ACS Chem Biol 15(8):2060–2069
Wu Z, Walsh C (1996) Dithiol compounds: potent, time-dependent inhibitors of VanX, a zinc-dependent D, D-dipeptidase required for vancomycin resistance in Enterococcus faecium. J Am Chem Soc 118(7):1785–1786
Wu Z, Wright GD, Walsh CT (1995) Overexpression, purification, and characterization of VanX, a D-, D-dipeptidase which is essential for vancomycin resistance in Enterococcus faecium BM4147. Biochemistry 34(8):2455–2463
Yang KW, Brandt JJ, Chatwood LL, Crowder MW (2000) Phosphonamidate and phosphothioate dipeptides as potential inhibitors of VanX. Bioorg Med Chem Lett 10(10):1085–1087
Yang KW, Cheng X, Zhao C, Liu CC, Jia C, Feng L, Xiao JM, Zhou LS, Gao HZ, Yang X, Zhai L (2011) Synthesis and activity study of phosphonamidate dipeptides as potential inhibitors of VanX. Bioorg Med Chem Lett 21(23):7224–7227
Zhang Z, Huang Q, Tao X, Song G, Zheng P, Li H, Sun H, Xia W (2019) The unique trimeric assembly of the virulence factor HtrA from Helicobacter pyloiri occurs via N-terminal domain swapping. J Biol Chem 294(20):7990–8000
Zhao BB, Li XH, Zeng YL, Lu YJ (2016) ClpP-deletion impairs the virulence of Legionella pneumophila and the optimal translocation of effector proteins. BMC Microbiol 16(1):1–2
Zhou X, Willems RJ, Friedrich AW, Rossen JW, Bathoorn E (2020) Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics. Antimicrob Resist Infect Control 9(1):1–3
Acknowledgements
The authors thank the Computational Biology Lab, Department of Bioinformatics, Bharathiar University for the computational facilities.
Funding
The authors have not disclosed any funding.
Author information
Authors and Affiliations
Contributions
SS conceptualization and writing, SP reviewing and proofing, NJ—reviewing and proofing.
Corresponding author
Ethics declarations
Conflict of interest
The authors have not disclosed any competing interests.
Additional information
Communicated by Yusuf Akhter.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Sundar, S., Piramanayagam, S. & Natarajan, J. A comprehensive review on human disease—causing bacterial proteases and their impeding agents. Arch Microbiol 205, 276 (2023). https://doi.org/10.1007/s00203-023-03618-5
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-023-03618-5