Abstract
The increasing antibiotic resistance is a clinical problem worldwide. Numerous Gram-negative bacteria have already become resistant to the most widely used class of antibacterial drugs, β-lactams. One of the main mechanisms is inactivation of β-lactam antibiotics by bacterial β-lactamases. Appearance and spread of these enzymes represent a continuous challenge for the clinical treatment of infections and for the design of new antibiotics and inhibitors. Drug repurposing is a prospective approach for finding new targets for drugs already approved for use. We describe here the inhibitory potency of known detoxifying antidote 2,3-dimercaptopropane-1-sulfonate (unithiol) against metallo-β-lactamases. Unithiol acts as a competitive inhibitor of meropenem hydrolysis by recombinant metallo-β-lactamase NDM-1 with the KI of 16.7 µM. It is an order of magnitude lower than the KI for l-captopril, the inhibitor of angiotensin-converting enzyme approved as a drug for the treatment of hypertension. Phenotypic methods demonstrate that the unithiol inhibits natural metallo-β-lactamases NDM-1 and VIM-2 produced by carbapenem-resistant K. pneumoniae and P. aeruginosa bacterial strains. The 3D full atom structures of unithiol complexes with NDM-1 and VIM-2 are obtained using QM/MM modeling. The thiol group is located between zinc cations of the active site occupying the same place as the catalytic hydroxide anion in the enzyme–substrate complex. The sulfate group forms both a coordination bond with a zinc cation and hydrogen bonds with the positively charged residue, lysine or arginine, responsible for proper orientation of antibiotics upon binding to the active site prior to hydrolysis. Thus, we demonstrate both experimentally and theoretically that the unithiol is a prospective competitive inhibitor of metallo-β-lactamases and it can be utilized in complex therapy together with the known β-lactam antibiotics.
Highlights
The microbial resistance to antibiotics represents an urgent problem of clinical medicine and pharmacology [1,2,3]
Their increasing prevalence is complicated by association of their genes with other resistance markers resulting in conferring the resistance to all known antibiotics [3]
We followed the strategy of drug repurposing to find new inhibitors of MBLs
Summary
The microbial resistance to antibiotics represents an urgent problem of clinical medicine and pharmacology [1,2,3]. Based on the structure of the active site, all β-lactamases are divided into serine-type and metal-dependent enzymes with one or two zinc ions in the active site [13,14]. The most clinically relevant MBLs belong to the subclass B1, and their widest geographical spread is attributed to the NDM type enzymes [18] Their increasing prevalence is complicated by association of their genes with other resistance markers resulting in conferring the resistance to all known antibiotics [3]. The search for MBL inhibitors is extremely intensive and involves various approaches targeting different structural elements of the enzymes. For MBLs, zinc ions are the most common target, and compounds containing one or several thiol groups demonstrate a high affinity for zinc cation and are actively studied as potential inhibitors [29,30,31]. We report the results on the combined experimental and computational study oscboeofaftmctththoepeferoiu1atu0hnpniictordhool,imdocuuolpncnboooprtiithitinffuonhaaegtu1nidiphno0undMireHinlndocsn,gtBio,edwghtauLrmhuwiseaondsicipoaslpniirNtlnoscu,ohfubgoDuwdgtiinnoerMensMeltntdtd,ahrreBts-wieieier1nnLapampraigalssonuseniirNpgwnrxfntdupoeaDdhtartdhVomsrietMebsuhInbdieMiergn-tytede1irsoeat-seeear2dlrufnrxsenoilbmanpzatdroysmyhguiftVnomiatrhibthnepniIheinaMdeoettetoshdsMdib-trceeM2iyasdmBsecgbkoBoexLfayufnompLdsilnrtztetihhbiyfsiNrtnf-eiehtimundmhDmedMesraieidMMiubutosBniigklecnBtL-ttxii1sderLo-mpN.edxaisnefsprenTDf.iriutuendsihhMmgrW tsheioamimir-oendbe1emnnoiet.s.tttlinoTiTmGaeesotslstchhsnreatatueeaten.anplhmdWmmatndorrGdo-doeicendnsrcos.mtaepythmTevmgoneapshipatclntar-eeerttuonmicdoiismstevvumapigiaeecletneaaicocrthvitnvdiaivtaenyrleoinbsscatamauomcsmdt simulations witshimthuelactoiomnsbiwnietdh qthueacnotmumbinmedecqhuaannictus/mmmoelecchualnaircsm/mecohleacnuilcasrpmoetechnatinailcss. potentials
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