ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores

Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia co ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation2CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP306943/2015-8; 420567/2016-099999.004913/2015-092015/15822-1; 2012/01953-9; 2016/05019-0; 2012/50161-8Precision Medicine Initiative (PRiME) at the University of Toronto internal fellowship [PMRF2019-007]; Canadian Institutes of Health Research (CIHR) postdoctoral fellowshipCanadian Institutes of Health Research (CIHR); CNPq-Brazil fellowship [202192/2015-6]; Saskatchewan Health Research Foundation postdoctoral fellowship; Ontario Graduate Scholarship (OGS)Ontario Graduate Scholarship; Department of Biochemistry at the University of Toronto; Centre for Pharmaceutical Oncology (University of Toronto); CIHR Training Program in Protein Folding and Interaction Dynamics: Principles and Diseases fellowshipCanadian Institutes of Health Research (CIHR) [TGF-53910]; University of Toronto Fellowship from the Department of Biochemistry; OGS fellowship; NSERC PGS-D2 fellowship; CIHR Emerging Team Grants from the Institute of Infection and ImmunityCanadian Institutes of Health Research (CIHR) [XNE-86945]; CIHR Project grantCanadian Institutes of Health Research (CIHR) [PJT-148564]; Global Affairs Canada (Canada); CAPES (Brazil)CAPES [99999.004913/2015-09]; NSERCNatural Sciences and Engineering Research Council of Canada [RGPIN-2015-04877, DG-20234]; Canada Research Chairs ProgramCanada Research Chairs; CIHR new investigator programCanadian Institutes of Health Research (CIHR); FAPESPFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2015/15822-1, 2012/01953-9, 2016/05019-0, 2012/50161-8]; CNPqNational Council for Scientific and Technological Development (CNPq) [306943/2015-8, 420567/2016-0]; AbbVie [1097737]; BayerBayer AG [1097737]; Boehringer IngelheimBoehringer Ingelheim [1097737]; Genome Canada through Ontario Genomics Institute GrantGenome Canada [1097737, OGI-055]; GlaxoSmithKlineGlaxoSmithKline [1097737]; JanssenJohnson & Johnson USAJanssen Biotech Inc [1097737]; Lilly CanadaEli Lilly [1097737]; MerckMerck & Company [1097737]; Novartis Research Foundation [1097737]; Ontario Ministry of Economic Development and Innovation [1097737]; PfizerPfizer [1097737]; TakedaTakeda Pharmaceutical Company Ltd [1097737]; Wellcome Trust GrantWellcome Trust [1097737, 092809/Z/10/Z]; Canada Foundation for InnovationCanada Foundation for Innovation; NSERCNatural Sciences and Engineering Research Council of Canada; University of Saskatchewan; Government of Saskatchewan; Western Economic Diversification Canada; National Research Council Canada; CIHRCanadian Institutes of Health Research (CIHR

Synthesis and Biological Evaluation of Antibacterial Small Molecule Activators of Caseinolytic Protease P and the Synthetic Utility of Metal Carboxylate Salts in Amidation Reactions with Amines

This thesis is presented in two parts and summarizes work carried out in the laboratory of Professor Robert A. Batey at the University of Toronto from September 2009 through March 2016. Part 1 of this thesis covers the synthesis and biological evaluation of two types of small molecules which target bacterial Caseinolytic Protease P (ClpP); these are the cyclic acyldepsipeptide (ADEP) class of antibiotics and related analogues (Chapter 2) and the ACP1 analogues (Chapter 3). Part 2 of this thesis outlines work related to the synthetic utility of metal carboxylate salts in amide bond-forming reactions with amines. Part 1 of this thesis begins with an introductory chapter (Chapter 1) on antibiotics to familiarize the reader with antibiotic classes, bacterial mechanisms of drug resistance as well as strategies for antibacterial drug discovery. Next, Chapter 2 details the total synthesis and biological evaluation of the A54556 ADEP natural products and related analogues. In the course of our investigations on this class of compound, a rapid two-step synthetic approach was developed that utilized a combination of solid-phase peptide chemistry and a novel lanthanide salt-promoted macrolactonization reaction. Importantly, this methodology was used to prepare several structurally diverse analogues. Chapter 3 then describes the synthesis and biological evaluation of ACP1 and related analogues. In contrast to the ADEPs, ACP1 was discovered using a high-throughput screen and several structurally unique analogues were synthesized in an attempt to improve potency and understand the structural features that impart biological activity. Part 2 of this thesis covers amidation reactions from the direct coupling of metal carboxylate salts with amines or ammonium salts in the presence of the coupling reagent HBTU (Chapter 4). A wide variety of carboxylate salts were examined and the methodology was later extended to multistep, one-pot variants using carboxylate salts that were generated in situ.Ph.D

Ruthenium-Catalyzed Asymmetric [2 + 2] Cycloadditions between Chiral Acyl Camphorsultam-Substituted Alkynes and Bicyclic Alkenes

Ruthenium-catalyzed asymmetric [2 + 2] cycloadditions between chiral acyl camphorsultam-functionalized alkynes and bicyclic alkenes were examined, providing adducts with complete <i>exo</i> stereoselectivity in good overall yield and enantioselectivity (up to 99% and 166:1, respectively), as well as appreciable diastereoselectivity (up to 163:1). The diastereoselectivity showed dependence on the solvent and temperature, as well as on the substitution pattern of the reacting alkyne and bicyclic alkene components. In general, higher diastereoselectivities were observed for reactions conducted in ethereal solvents and at lower temperatures between <i>N</i>-propynoyl camphorsultams and bicyclic alkenes

High-spin supramolecular pair of Mn(II)/thiazyl radical complexes

TheMn(hfac)2 complex of the paramagnetic 4-(benzoxazol-20-yl)-1,2,3,5-dithiadiazolyl ligand is reported (hfac = 1,1,1,5,5,5- hexafluoroacetylacetonato-). The Mn(II) and radical ligand spins are coupled antiferromagnetically (AF) in the coordination complex. Short sulfur–oxygen contacts between molecules provide an efficient pathway for AF coupling between the radical ligand of one molecule and the Mn(II) of a neighbouring molecule, resulting in a large total spin ground state (ST = 4) for a pair of molecules

A Lanthanide(III) Triflate Mediated Macrolactonization/Solid-Phase Synthesis Approach for Depsipeptide Synthesis

The effect of dysprosium­(III) triflate on macrolactonization reactions to form depsipeptides using MNBA (Shiina’s reagent) is reported. Improved yields were obtained for the formation of 16-membered depsipeptides using lanthanide triflate additives. The use of a macrocyclization strategy permits the use of a semiautomated solid-phase synthesis approach for the rapid synthesis of analogues of the antibacterial A54556 acyldepsipeptides in only two physical operations, requiring only final product purification after cyclization

Amidation Reactions from the Direct Coupling of Metal Carboxylate Salts with Amines

A general method for the synthesis of amides involving the direct coupling of alkali metal carboxylate salts with amines is described. Amidation of a wide variety of carboxylate salts with either free amines or their ammonium hydrochloride salts can be achieved using HBTU as a coupling agent in combination with Hünig’s base. The reaction is highly efficient and is generally complete in as little as 1–2 h, giving the products in good to excellent yields. The protocol is valuable for the coupling of carboxylates for which the corresponding carboxylic acids or acyl chlorides are unstable, less conveniently manipulated/isolated, or are not commercially available. For example, the coupling of amines and α-amino acids with lithium 5-bromo-1<i>H</i>-pyrrole-2-carboxylate, whose corresponding acid that is prone to decarboxylation, allowed for the synthesis of 5-bromo-1<i>H</i>-pyrrole-2-carboxamides, which are analogues of the pyrrole-2-aminoimidazole marine alkaloids. The protocol can be combined with other reactions in a sequenced fashion, as exemplified by the synthesis of acetylenic amides, in a one-pot procedure, via the coupling of a lithium carboxylate salt formed initially by the addition of carbon dioxide to a lithiated terminal alkyne

Total Synthesis and Antibacterial Testing of the A54556 Cyclic Acyldepsipeptides Isolated from <i>Streptomyces hawaiiensis</i>

The first total synthesis of all six known A54556 acyldepsipeptide (ADEP) antibiotics from <i>Streptomyces hawaiiensis</i> is reported. This family of compounds has a unique mechanism of antibacterial action, acting as activators of caseinolytic protease (ClpP). Assembly of the 16-membered depsipeptide core was accomplished via a pentafluorophenyl ester-based macrolactamization strategy. Late stage amine deprotection was carried out under neutral conditions by employing a mild hydrogenolysis strategy, which avoids the formation of undesired ring-opened depsipeptide side products encountered during deprotection of acid-labile protecting groups. The free amines were found to be significantly more reactive toward late stage amide bond formation as compared to the corresponding ammonium salts, giving final products in excellent yields. A thorough NMR spectroscopic analysis of these compounds was carried out to formally assign the structures and to aid with the spectroscopic assignment of ADEP analogues. The identity of two of the structures was confirmed by comparison with biologically produced samples from <i>S. hawaiiensis</i>. An X-ray crystallographic analysis of an ADEP analogue reveals a conformation similar to that found in cocrystal structures of ADEPs with ClpP protease. The degree of antibacterial activity of the different compounds was evaluated <i>in vitro</i> using MIC assays employing both Gram-positive and Gram-negative strains and a fluorescence-based biochemical assay

Total Synthesis and Antibacterial Testing of the A54556 Cyclic Acyldepsipeptides Isolated from <i>Streptomyces hawaiiensis</i>

The first total synthesis of all six known A54556 acyldepsipeptide (ADEP) antibiotics from <i>Streptomyces hawaiiensis</i> is reported. This family of compounds has a unique mechanism of antibacterial action, acting as activators of caseinolytic protease (ClpP). Assembly of the 16-membered depsipeptide core was accomplished via a pentafluorophenyl ester-based macrolactamization strategy. Late stage amine deprotection was carried out under neutral conditions by employing a mild hydrogenolysis strategy, which avoids the formation of undesired ring-opened depsipeptide side products encountered during deprotection of acid-labile protecting groups. The free amines were found to be significantly more reactive toward late stage amide bond formation as compared to the corresponding ammonium salts, giving final products in excellent yields. A thorough NMR spectroscopic analysis of these compounds was carried out to formally assign the structures and to aid with the spectroscopic assignment of ADEP analogues. The identity of two of the structures was confirmed by comparison with biologically produced samples from <i>S. hawaiiensis</i>. An X-ray crystallographic analysis of an ADEP analogue reveals a conformation similar to that found in cocrystal structures of ADEPs with ClpP protease. The degree of antibacterial activity of the different compounds was evaluated <i>in vitro</i> using MIC assays employing both Gram-positive and Gram-negative strains and a fluorescence-based biochemical assay