Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors.

Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocke…

Synthesis of a Fullerene Derivative of Benzo[18]crown-6 byDiels-Alder Reaction: Complexation Ability, Amphiphilic Properties, and X-Ray Crystal Structure of a Dimethoxy-1,9-(methano[1,2]benzenomethano)fullerene[60] Benzene Clathrate

A fullerene derivative 1 of benzo[18]crown-6 was obtained by Diels-Alder addition of fullerene[60](C60) to the ortho-quinodimethane prepared in situ from 4,5-bis(bromomethyl)benzo[18]crown-6 (3) with Bu4NI in toluene. Extraction experiments show that the complexation of K+ ions strongly increases the solubility of 1 in protic solvents like MeOH. Using Langmuir-Blodgett techniques, monolayers of the highly amphiphilic fullerene-derived crown ether 1 and its K+ ion complex were prepared. An X-ray crystal structure was obtained from a benzene clathrate of comparison compound 2, synthesized by Diels-Alder reaction of C60 with the ortho-quinodimethane derived from 1,2-bis(bromomethyl)-4,5-dimeth…

Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings on Peptide Amide Bonds

The π-stacking of fluorinated benzene rings on protein backbone amide groups was investigated, using a dual approach comprising enzyme-ligand binding studies complemented by high-level quantum chemical calculations. In the experimental study, the phenyl substituent of triazine nitrile inhibitors of human cathepsin L (hCatL), which stacks onto the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket, was systematically fluorinated, and differences in inhibitory potency were measured in a fluorimetric assay. Binding affinity is influenced by lipophilicity (clog P), the dipole and quadrupole moments of the fluorinated rings, but also by additional interactions of the introduced fluo…

Synthesis of a Fullerene[60] Cryptate and Systematic Langmuir-Blodgett and Thin-Film Investigations of Amphiphilic Fullerene Derivatives

The synthesis of the first fullerene cryptate 7 with a sodium ion bound to a benzo[2.2.2]cryptand covalently attached to a methanofullerene[60] is described. The amphiphilic properties of 7 as well as of a variety of other covalent fullerene derivatives with polar functional groups and the ability of these compounds to form Langmuir monolayers at the air-water interface were investigated in a systematic study. Among these derivatives are Diels-Alder adducts of C60 and methanofullerenes, four of which are fullerene C-glycosides. The films at the water surface were characterized by their surface pressure versus molecular area isotherms, compression and expansion cycles, and optical light micr…

Systematic Investigation of Resorcin[4]arene-Based Cavitands as Affinity Materials on Quartz Crystal Microbalances.

Resorcin[4]arene cavitands are well-known supramolecular hosts, and their outstanding guest-binding abilities in solution have been studied in detail in recent decades. In a systematic approach, different resorcin[4]arene cavitands and container molecules are characterized as affinity materials for gravimetric sensing using high-fundamental-frequency quartz crystal microbalances. Analysis of their affinity toward a series of various analytes reveals a remarkable dependence of both selectivity and sensitivity on the shape, accessibility, and size of the cavity, along with their supramolecular interactions with the host molecules.

Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the S3 Pocket.

We report an extensive "heteroarene scan" of triazine nitrile ligands of the cysteine protease human cathepsin L (hCatL) to investigate π-stacking on the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket. This heteroarene⋅⋅⋅peptide bond stacking was supported by a co-crystal structure of an imidazopyridine ligand with hCatL. Inhibitory constants (Ki ) are strongly influenced by the diverse nature of the heterocycles and specific interactions with the local environment of the S3 pocket. Binding affinities vary by three orders of magnitude. All heteroaromatic ligands feature enhanced binding by comparison with hydrocarbon analogues. Predicted energetic contributions from the ori…

Tetraethynylethene molecular scaffolding: Nonlinear optical, redox, and amphiphilic properties of donor functionalized polytriacetylene and expanded radialenes

Tuning and Predicting Biological Affinity: Aryl Nitriles as Cysteine Protease Inhibitors

A series of aryl nitrile-based ligands were prepared to investigate the effect of their electrophilicity on the affinity against the cysteine proteases rhodesain and human cathepsin L. Density functional theory calculations provided relative reactivities of the nitriles, enabling prediction of their biological affinity and cytotoxicity and a clear structure-activity relationship.

Cryogenic 35GHz pulse ENDOR probehead accommodating large sample sizes: Performance and applications.

The construction and performance of a cryogenic 35GHz pulse electron nuclear double resonance (ENDOR) probehead for large samples is presented. The resonator is based on a rectangular TE(102) cavity in which the radio frequency (rf) B(2)-field is generated by a two turn saddle ENDOR coil crossing the resonator along the sample axis with minimal distance to the sample tube. An rf power efficiency factor is used to define the B(2)-field strength per square-root of the transmitted rf power over the frequency range 2-180MHz. The distributions of the microwave B(1)- and E(1)-field, and the rf B(2)-field are investigated by electromagnetic field calculations. All dielectrics, the sample tube, and…

A Fluorine Scan at the Catalytic Center of Thrombin: CF, COH, and COMe Bioisosterism and Fluorine Effects on pKa and logD Values

A series of 16 tricyclic thrombin inhibitors was prepared by using the 1,3-dipolar cycloaddition of azomethine ylides derived from 3- or 4-hydroxyproline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide as the key step. The terminal pyrrolidine ring of the inhibitors was systematically substituted to explore the potential bioisosteric behavior of C-F, C-OH, and C-OMe residues pointing into the environment of the catalytic center of a serine protease. X-ray crystal structure analyses revealed a distinct puckering preference of this ring. Substitution by F, HO, and MeO has a strong effect on the basicity of the adjacent pyrrolidine nitrogen center which originates from two sigma-indu…

ChemInform Abstract: Synthesis of a Fullerene Derivative of Benzo(18)crown-6 by Diels-Alder Reaction: Complexation Ability, Amphiphilic Properties, and X-Ray Crystal Structure of a Dimethoxy-1,9-(methano(1,2)benzenomethano) fullerene(60) Benzene Clathrate

A fullerene derivative 1 of benzo[18]crown-6 was obtained by Diels-Alder addition of fullerene[60](C60) to the ortho-quinodimethane prepared in situ from 4,5-bis(bromomethyl)benzo[18]crown-6 (3) with Bu4NI in toluene. Extraction experiments show that the complexation of K+ ions strongly increases the solubility of 1 in protic solvents like MeOH. Using Langmuir-Blodgett techniques, monolayers of the highly amphiphilic fullerene-derived crown ether 1 and its K+ ion complex were prepared. An X-ray crystal structure was obtained from a benzene clathrate of comparison compound 2, synthesized by Diels-Alder reaction of C60 with the ortho-quinodimethane derived from 1,2-bis(bromomethyl)-4,5-dimeth…

Predicting and Tuning Physicochemical Properties in Lead Optimization: Amine Basicities

This review describes simple and useful concepts for predicting and tuning the pK(a) values of basic amine centers, a crucial step in the optimization of physical and ADME properties of many lead structures in drug-discovery research. The article starts with a case study of tricyclic thrombin inhibitors featuring a tertiary amine center with pK(a) values that can be tuned over a wide range, from the usual value of around 10 to below 2 by (remote) neighboring functionalities commonly encountered in medicinal chemistry. Next, the changes in pK(a) of acyclic and cyclic amines upon substitution by fluorine, oxygen, nitrogen, and sulfur functionalities, as well as carbonyl and carboxyl derivativ…

Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors.

Rhodesain (RD) is a parasitic, human cathepsin L (hCatL) like cysteine protease produced by Trypanosoma brucei (T. b.) species and a potential drug target for the treatment of human African trypanosomiasis (HAT). A library of hCatL inhibitors was screened, and macrocyclic lactams were identified as potent RD inhibitors (Ki < 10 nM), preventing the cell-growth of Trypanosoma brucei rhodesiense (IC50 < 400 nM). SARs addressing the S2 and S3 pockets of RD were established. Three cocrystal structures with RD revealed a noncovalent binding mode of this ligand class due to oxidation of the catalytic Cys25 to a sulfenic acid (Cys–SOH) during crystallization. The P-glycoprotein efflux ratio was mea…

Optimization of Triazine Nitriles as Rhodesain Inhibitors: Structure-Activity Relationships, Bioisosteric Imidazopyridine Nitriles, and X-ray Crystal Structure Analysis with Human Cathepsin L

The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 subs…

Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl groups into the p pocket.

In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics f…

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors.

Improving the binding affinity of a chemical series by systematically probing one of its exit vectors is a medicinal chemistry activity that can benefit from molecular modeling input. Herein, we compare the effectiveness of four approaches in prioritizing building blocks with better potency: selection by a medicinal chemist, manual modeling, docking followed by manual filtering, and free energy calculations (FEP). Our study focused on identifying novel substituents for the apolar S2 pocket of cathepsin L and was conducted entirely in a prospective manner with synthesis and activity determination of 36 novel compounds. We found that FEP selected compounds with improved affinity for 8 out of …

2 H-1,2,3-Triazole-Based Dipeptidyl Nitriles: Potent, Selective, and Trypanocidal Rhodesain Inhibitors by Structure-Based Design.

Macrocyclic inhibitors of rhodesain (RD), a parasitic cysteine protease and drug target for the treatment of human African trypanosomiasis, have shown low metabolic stability at the macrocyclic ether bridge. A series of acyclic dipeptidyl nitriles was developed using structure-based design (PDB ID: 6EX8). The selectivity against the closely related cysteine protease human cathepsin L (hCatL) was substantially improved, up to 507-fold. In the S2 pocket, 3,4-dichlorophenylalanine residues provided high trypanocidal activities. In the S3 pocket, aromatic residues provided enhanced selectivity against hCatL. RD inhibition (Ki values) and in vitro cell-growth of Trypanosoma brucei rhodesiense (I…

CCDC 916055: Experimental Crystal Structure Determination

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CCDC 1516759: Experimental Crystal Structure Determination

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CCDC 1516756: Experimental Crystal Structure Determination

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