Crystal structure of a squalene cyclase in complex with the potential anticholesteremic drug Ro48-8071

Squalene-hopene cyclase (SHC) catalyzes the conversion of squalene into pentacyclic compounds. It is the prokaryotic counterpart of the eukaryotic oxidosqualene cyclase (OSC) that catalyzes the steroid scaffold formation. Because of clear sequence homology, SHC can serve as a model for OSC, which is an attractive target for anticholesteremic drugs. We have established the crystal structure of SHC complexed with Ro48-8071, a potent inhibitor of OSC and therefore of cholesterol biosynthesis. Ro48-8071 is bound in the active-center cavity of SHC and extends into the channel that connects the cavity with the membrane. The binding site of Ro48-8071 is largely identical with the expected site of squalene; it differs from a previous model based on photoaffinity labeling. The knowledge of the inhibitor binding mode in SHC is likely to help develop more potent inhibitors for OSC.     

The binding site for an inhibitor of squalene:hopene cyclase determined using photoaffinity labeling and molecular modeling.

BACKGROUND: The squalene:hopene cyclases (SHCs) are bacterial enzymes that convert squalene into hopanoids, a function analogous to the action of oxidosqualene cyclases (OSCs) in eukaryotic steroid and triterpenoid biosynthesis. We have identified the binding site for a selective, potent, photoactivatable inhibitor of an SHC. RESULTS: SHC from Alicyclobacillus acidocaldarius was specifically labeled by [3H]Ro48-8071, a benzophenone-containing hypocholesteremic drug. Edman degradation of a peptide fragment of covalently modified SHC confirmed that Ala44 was specifically modified. Molecular modeling, using X-ray-derived protein coordinates and a single point constraint for the inhibitor, suggested several geometries by which Ro48-8071 could occupy the active site. CONCLUSIONS: A covalent complex of a potent inhibitor with a squalene cyclase has been characterized. The amino acid modification and molecular modeling suggest that Ro48-8071 binds at the junction between the central cavity and substrate entry channel, therefore inhibiting access of the substrate to the active site.     

Site-directed mutagenesis of squalene-hopene cyclase: altered substrate specificity and product distribution

BACKGROUND: Two regions of squalene-hopene cyclase (SHC) were examined to define roles for motifs posited to be responsible for initiation and termination of the enzyme-catalyzed polyolefinic cyclizations. Specifically, we first examined the triple mutant of the DDTAVV motif, a region deeply buried in the catalytic cavity and thought to be responsible for the initiation of squalene cyclization. Next, four mutants were prepared for Glu45, a residue close to the substrate entrance channel proposed to be involved in the termination of the cyclization of squalene. RESULTS: The DDTAVV motif in SHC was changed to DCTAEA, the corresponding conserved region of eukaryotic oxidosqualene cyclase (OSC), by the triple mutation of D377C/V380E/V381A; selected single mutants were also examined. The triple mutant showed no detectable cyclization of squalene, but effectively cyclized 2,3-oxidosqualene to give mono- and pentacyclic triterpene products. Of the Glu45 mutants, E45A and E45D showed reduced activity, E45Q showed slightly increased activity, and E45K was inactive. A normal yield of pentacyclic products was produced, but the ratio of hopene 2 to hopanol 3 was significantly changed in the less active mutants. CONCLUSIONS: Initiation and substrate selectivity may be determined by the interaction of the DDTAVV motif with the isopropylidene of squalene (for SHC) and of the DCTAEA motif with the epoxide of oxidosqualene (for OSC). This is the first report of a substrate switch determined by a central catalytic motif in a triterpenoid cyclase. At the termination of cyclization, the product ratio may be largely controlled by Glu45 at the entrance channel to the active site.     

Enzymatic cyclization of 26- and 27-methylidenesqualene to novel unnatural C31 polyprenoids by squalene:hopene cyclase

Squalene:hopene cyclase (SHC) from Alicyclobacillus acidocaldarius accepted 26-methylidenesqualene (26-MS) and 27-methylidenesqualene (27-MS) as a substrate and converted to novel pentacyclic C₃₁ polyprenoids; a dammarene derivative with a 6.6.6.5+6 ring system and 26-methylidene-hop-22(29)-ene, respectively. The broad substrate specificity of the enzyme provided important information on the structure and function of SHC. Interestingly, 27-MS was also found to be a potent inhibitor of the bacterial SHC (IC₅₀=5 μM), while 26-MS just showed poor enzyme inhibition (IC₅₀=ca. 100 μM).     

Cation-pi interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase

It has been assumed that the pi-electrons of aromatic residues in the catalytic sites of triterpene cyclases stabilize the cationic intermediates formed during the polycyclization cascade of squalene or oxidosqualene, but no definitive experimental evidence has been given. To validate this cation-pi interaction, natural and unnatural aromatic amino acids were site-specifically incorporated into squalene-hopene cyclase (SHC) from Alicyclobacillus acidocaldarius and the kinetic data of the mutants were compared with that of the wild-type SHC. The catalytic sites of Phe365 and Phe605 were substituted with O-methyltyrosine, tyrosine, and tryptophan, which have higher cation-pi binding energies than phenylalanine. These replacements actually increased the SHC activity at low temperature, but decreased the activity at high temperature, as compared with the wild-type SHC. This decreased activity is due to the disorganization of the protein architecture caused by the introduction of the amino acids more bulky than phenylalanine. Then, mono-, di-, and trifluorophenylalanines were incorporated at positions 365 and 605; these amino acids reduce cation-pi binding energies but have van der Waals radii similar to that of phenylalanine. The activities of the SHC variants with fluorophenylalanines were found to be inversely proportional to the number of the fluorine atoms on the aromatic ring and clearly correlated with the cation-pi binding energies of the ring moiety. No serious structural alteration was observed for these variants even at high temperature. These results unambiguously show that the pi-electron density of residues 365 and 605 has a crucial role for the efficient polycyclization reaction by SHC. This is the first report to demonstrate experimentally the involvement of cation-pi interaction in triterpene biosynthesis.     

Chemo-enzymatic syntheses of drimane-type sesquiterpenes and the fundamental core of hongoquercin meroterpenoid by recombinant squalene-hopene cyclase

Squalene-hopene cyclase (SHC) converts squalene (C(30)) into pentacyclic triterpenes of hopene and hopanol. A linear sesquiterpene, (6E,10E)-2,6,10-trimethyldodeca-2,6,10-triene, underwent cyclization catalyzed by SHC, affording the following six bicyclic sesquiterpenes (drimane skeleton) in relatively high yield (68%): drim-7(8)-ene, drim-8(12)-ene, drim-8(9)-ene, driman-8α-ol, driman-8β-ol, and the novel sesquiterpene, named quasiclerodane, the skeleton of which is analogous to that of clerodane diterpene. To extend the scope of the enzymatic syntheses, acyclic sesquiterpenes to which a phenol moiety was appended were subjected to the enzymatic reaction catalyzed by SHC. The cyclic meroterpene core present in hongoquercins A and B was successfully prepared. The formation mechanisms of drimane-type sesquiterpenes and the cyclic meroterpene core of hongoquercins A and B are discussed.     

Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring

To provide insight into the polycyclization mechanism of squalene by squalene-hopene cyclase (SHC) from Alicyclobacilus acidocaldarius, some analogs of nor- and bisnorsqualenes were synthesized including the deuterium-labeled squalenes and incubated with the wild-type SHC, leading to the following inferences. (1) The deprotonation reaction for the introduction of the double bond of the hopene skeleton occurs exclusively from the Z-methyl group on the terminal double bond of squalene. (2) 3R-Oxidosqualene was folded in a boat conformation for the A-ring construction, while the 3S-form was in a chair structure. (3) The terminal two methyl groups are indispensable both for the formation of the 5-membered E-ring of the hopene skeleton and for the initiation of the polycyclization cascade, but the terminal Z-methyl group has a more crucial role for the construction of the 5-membered E-ring than the E-methyl group. (4) Some of the novel terpene skeletons, 36, 37, 39 and 40, were created from the analogs employed in this investigation.     

Cover Picture: Harnessing the Structure and Dynamics of the Squalene-Hopene Cyclase for (−)-Ambroxide Production (Angew. Chem. Int. Ed. 22/2023)

Terpene cyclases offer enormous synthetic potential, given their unique ability to forge complex hydrocarbon scaffolds from achiral precursors within a single cationic rearrangement cascade. Harnessing their synthetic power, however, has proved to be challenging owing to their generally low catalytic performance. In this study, we unveiled the catalytic potential of the squalene-hopene cyclase (SHC) by harnessing its structure and dynamics. First, we synergistically tailored the active site and entrance tunnel of the enzyme to generate a 397-fold improved (−)-ambroxide synthase. Our computational investigations explain how the introduced mutations work in concert to improve substrate acquisition, flow, and chaperoning. Kinetics, however, showed terpene-induced inactivation of the membrane-bound SHC to be the major turnover limitation in vivo. Merging this insight with the improved and stereoselective catalysis of the enzyme, we applied a feeding strategy to exceed 10⁵ total turnovers. We believe that our results may bridge the gap for broader application of SHCs in synthetic chemistry.     

Structure activity relationships of new inhibitors of mammalian 2,3-oxidosqualene cyclase designed from isoquinoline derivatives

We have designed more potent inhibitors from the previously reported LF 05-0038, a 6-isoquinolinol based inhibitor of 2,3-oxidosqualene cyclase (IC50: 1.1 microM). Replacement of the 3-OH group by various 3-substituted amino groups, and modification of the alkyl chain borne by the endocyclic nitrogen led to inhibitors with IC50 in the range of 0.15 to 1 microM. In a second step, opening of the bicyclic ring system afforded the corresponding aminoalkylpiperidines which were slightly more potent. Finally, introduction of suitable aromatic containing moieties on the piperidine nitrogen yielded very potent inhibitors such as 20x (IC50 = 18 nM) easy to synthesize and achiral. The recent availability of the crystal structure of squalene-hopene cyclase allowed us to construct a three-dimensional (3D) model of the related 2,3-oxidosqualene cyclase (OSC) which was tentatively used to describe the possible mode of binding of our compounds and which can be useful for designing new inhibitors.     

Mechanistic insights into oxidosqualene cyclizations through homology modeling

2,3-Oxidosqualene cyclases (OSC) are key enzymes in sterol biosynthesis. They catalyze the stereoselective cyclization and skeletal rearrangement of (3S)-2,3-oxidosqualene to lanosterol in mammals and fungi and to cycloartenol in algae and higher plants. Sequence information and proposed mechanism of 2,3-oxidosqualene cyclases are closely related to those of squalene-hopene cyclases (SHC), which represent functional analogs of OSCs in bacteria. SHCs catalyze the cationic cyclization cascade converting the linear triterpene squalene to fused ring compounds called hopanoids. High stereoselectivity and precision of the skeletal rearrangements has aroused the interest of researchers for nearly half a century, and valuable data on studying mechanistic details in the complex enzyme-catalyzed cyclization cascade has been collected. Today, interest in cyclases is still unbroken, because OSCs became targets for the development of antifungal and hypocholesterolemic drugs. However, due to the large size and membrane-bound nature of OSCs, three-dimensional structural information is still not available, thus preventing a complete understanding of the atomic details of the catalytic mechanism. In this work, we discuss results gained from homology modeling of human OSC based on structural information of SHC from Alicyclobacillus acidocaldarius and propose a structural model of human OSC. The model is in accordance with previously performed experimental studies with mechanism-based suicide inhibitors and mutagenesis experiments with altered activity and product specificity. Structural insight should strongly stimulate structure-based design of antifungal or cholesterol-lowering drugs.     

Balancing kinetic and thermodynamic control: the mechanism of carbocation cyclization by squalene cyclase

Molecular dynamics simulations with a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the squalene-to-hopene carbocation cyclization mechanism in squalene-hopene cyclase (SHC). The present study is based on free energy simulations by constructing the free energy surface for the cyclization steps along the reaction pathway. The picture that emerges for the carbocation cyclization cascade is a delicate balance of thermodynamic and kinetic control that ultimately favors the formation of the final hopanoids carbon skeleton. A key finding is that the five- to six-membered ring expansion process is not a viable reaction pathway for either C- or D-ring formation in the cyclization reaction. The only significant intermediate is the A/B-bicyclic cyclohexyl cation (III), from which two asynchronous concerted reaction pathways lead to, respectively, the 6,6,6,5-tetracyclic carbon skeleton and the 6,6,6,6,5-pentacyclic hopanoids. Experimentally, these two products are observed to have 1% and 99% yields, respectively, in the wild-type enzyme. We conclude that the product distribution in the wild-type enzyme is dictated by kinetic control of these two reaction pathways.     

Phenomenological kinetics of the thermal decomposition of sodium hydrogencarbonate

Aiming to find rigorous understanding and novel features for their potential applications, the physico-geometrical kinetics of the thermal decomposition of sodium hydrogencarbonate (SHC) was investigated by focusing on the phenomenological events taking place on a single crystalline particle during the course of the reaction. The overall kinetics evaluated by systematic measurements of the kinetic rate data by thermogravimetry under carefully controlled conditions were interpreted in association with the morphological studies on the precursory reaction, mechanism of surface reaction, structure of the surface product layer, diffusion path of evolved gases, crystal growth of the solid product, and so on. The precursory reaction was identified as the decomposition of impurity, taking place at the boundary between the surface of the SHC crystal and the adhesive small SHC particles deposited on the surface. In flowing dry N(2), the thermal decomposition of SHC proceeds by two-dimensional shrinkage of the reaction interface controlled by chemical reaction with the apparent activation energy of about 100 kJ mol(-1), after rapid completion of the surface reaction and formation of porous surface product layer. Atmospheric CO(2) and water vapor influence differently on the overall kinetics of the thermal decomposition of SHC. Added gas phase of CO(2) slightly inhibits the overall rate because of the increasing contribution of the surface reaction. Under higher water vapor pressure, the physico-geometrical mechanism of the surface reaction changes drastically, indicating the preliminary reformation of reactant surface and the formation of needle crystals of solid product on the surface. The mechanistic change and extended contribution of the surface reaction result in the deceleration of the surface reaction and acceleration of the established reaction.     

Identifying hQC Inhibitors of Alzheimer’s Disease by Effective Customized Pharmacophore-Based Virtual Screening,Molecular Dynamic Simulation,and Binding Free Energy Analysis

Applied Biochemistry and Biotechnology - Human glutaminyl cyclase (hQC) appeared as a promising new target with its inhibitors attracted much attention for the treatment of Alzheimer’s...     

正己烷存在下的氢选择性催化燃烧

以正己烷作为裂解原料烃类代表,Pt-Sn/Al₂O₃催化剂作为氢选择性燃烧催化剂,对直接内加热方式提供热量促使裂解原料达到可裂解温度的可行性进行了研究。结果表明,温度相同时,Pt-Sn/Al₂O₃ 催化剂存在时氢燃烧的选择性明显高于无催化剂存在时的非催化氢燃烧过程,Pt-Sn/Al₂O₃ 催化剂是优良的氢选择性燃烧催化剂。该催化剂在催化氢选择性燃烧过程中,存在一个临界温度点650℃。当物流入口温度低于650℃时,氢燃烧选择性达90%以上;高于650℃时,由于非催化氢燃烧所占总燃烧反应比例加大,造成氢燃烧选择性有所降低。同时,在一定温度下,要获得高的氢燃烧选择性及氧气转化率,须综合考虑氢烃比和氢氧比的影响。     

A molecular insight into deoiled asphalt’s slurry-phase hydrocracking process

Qilu vacuum residue with Ni + V content of 120 ppm and Ca content of 40 ppm, is hard to process for fixed bed hydrocracking technology. In this work, solvent deasphalting process was used as a pretreatment for processing Qilu vacuum residue, and the yield of deasphalted oil could be up to 48.3 %, with less metal (Ni + V + Ca < 15 ppm) and asphaltene (<0.1 %) in deasphalted oil. The n-butane solvent in solvent deasphalting (SDA) process had higher selectivity for HC class, and correspondingly the relative abundance of HC class of deasphalted oil (DAO) was much higher than that of deasphalted oil (DAO). The abundance of DAO was higher than that of DOA when double bond equivalent (DBE) < 14 or carbon number (CN) < 46, and the relative abundance of SDA1-DOA was higher than that of SDA2-DOA when DBE < 20 or CN < 46. Deoiled asphalt was taken as the feed of slurry-phase hydrocracking (SHC) process, and the conversion ratio of deoiled asphalt in slurry-phase hydrocracking process could be more than 80 % for 240 min reaction. The conversion ratios of SDA1-DOA for SHC1-120 min and SHC1-240 min reactions were 66.92 % and 81.64 % respectively, and the conversion ratios of SDA2-DOA for SHC2-120 min and SHC2-240 min reactions were 70.19 % and 85.71 % respectively. Sulfur species and asphaltene changing rules at molecular level were determined to evaluate DOA’s slurry-phase hydrocracking process.     

Effect of metabolic inhibitors on vasopressin-stimulated transport systems in the toad bladder.

Vasopressin increases the permeability of receptor cells to water and, in tissues such as toad bladder, to solutes such as urea. While cyclic AMP appears to play a major role in mediating the effects of vasopressin, there is evidence that activation of the water permeability system and the urea permeability system involves separate pathways. In the present study, we have shown that inhibitors of oxidative metabolism (rotenone, dinitrophenol, and methylene blue) selectively inhibit either vasopressin-stimulated water flow or vasopressin-stimulated urea transport. There was no inhibition, however, when exogenous cyclic AMP was substituted for vasopressin, and little to no inhibition when the potent analogue 8-bromoadenosine 3',5'-cyclic monophosphate (8-Br-cAMP) was employed. Rotenone had no effect on adenylate cyclase activity or cyclic AMP levels within the cell; dinitrophenol decreased adenylate cyclase activity minimally. Additional studies with vinblastine and nocodazole, inhibitors of microtubule assembly, demonstrated an inhibition of vasopressin and cyclic AMP-stimulated water flow but showed no effect on urea transport. We would conclude that water and urea transport, as examples of hormone-stimulated processes, have different links to cell metabolism, and that in addition to cyclic AMP, a non-nucleotide pathway may be involved in the action of vasopressin.     

Addition of S‐Heterocyclic Carbenes to Fullerenes: Formation and Characterization of Dithiomethano‐Bridged Derivatives

The reactions of novel S‐heterocyclic carbenes (SHCs), which were prepared by the cycloaddition of disilenes and digermenes to CS₂, with C₆₀ and Sc₃N@I_h‐C₈₀ afforded the corresponding methano‐bridged fullerenes. The [6,6]‐closed and [6,6]‐open structures were characterized for the SHC adducts of C₆₀ and Sc₃N@I_h‐C₈₀, respectively. These derivatives exhibited relatively low oxidation potentials, indicative of the electron‐donating effects of the SHC addends. The electronic properties of the SHC derivatives were clarified by the density functional theory calculations.     

Fluorescence-based adenylyl cyclase assay adaptable to high throughput screening

The second messenger cAMP has been implicated in numerous cellular processes such as glycogen metabolism, muscle contraction, learning and memory, and differentiation and development. Genetic evidence suggests that the enzyme that produces cAMP, adenylyl cyclase (AC), may be involved in pathogenesis in many of these cellular processes. In addition, these data suggest that membrane-bound ACs may be valuable targets for therapeutics to treat pathogenesis of these processes. The development of a robust real-time adenylyl cyclase assay that can be scalable to high-throughput screening could help in the development of novel therapeutics. Here we report a novel fluorescence-based cyclase assay using Bodipy FL GTPgammaS (BGTPgammaS). The fluorescence of the Bodipy moiety of BGTPgammaS was dramatically enhanced by incubation with the minimal catalytic core of wild-type-AC (wt-AC) and a mutant with decreased purine selectivity (mut-AC), in an AC activation-dependent manner. No increase in fluorescence was observed using Bodipy FL ATPgammaS (BATPgammaS) as substrate for either wt-AC or mut-AC. Using BGTPgammaS, forskolin, Gsalpha.GTPgammaS and the divalent cation Mn(2+) potently enhanced the rate of fluorescence increase in a concentration-dependent manner. The fluorescence enhancement of the Bodipy moiety was inhibited by known inhibitors of AC such as 2'deoxy,3'AMP and 2',5'-dideoxy-3'ATP. Furthermore, the fluorescence assay is adaptable to 96-well and 384-well multiplate format and is thus applicable to high throughput screening methodologies.     

The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis

The class II chelatase CfbA catalyzes Ni²⁺ insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni²⁺ and Co²⁺ remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni²⁺, Ni-SHC, and Co²⁺ were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni²⁺-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co²⁺ than Ni²⁺. Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni²⁺ and Co²⁺ by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni²⁺ insertion catalytic mechanism was proposed: Ni²⁺ insertion to SHC is promoted by the support of an acetate side chain of SHC.

The substrate-assisted nickel chelatase mechanism of CfbA in coenzyme F430 biosynthesis was unveiled by X-ray crystal structure analysis.     

Novel nicotinamide adenine dinucleotide analogues as selective inhibitors of NAD-dependent enzymes

Three novel dinucleotide analogues of nicotinamide adenine dinucleotide (NAD⁺) have been synthesised from d-ribonolactone. These compounds incorporate a thiophene moiety in place of nicotinamide and are hydrolytically stable. They have been evaluated as inhibitors of adenosine diphosphate ribosyl cyclase, glutamate dehydrogenase and Sir2 acyltransferase activities. Enzyme specificity and a high level of inhibition was observed for the dehydrogenase.