Model complexes of cobalt-substituted matrix metalloproteinases: tools for inhibitor design

The tetrahedral cobalt(II) complex [(Tp(Ph,Me))CoCl] (Tp(Ph,Me) = hydrotris(3,5-phenylmethylpyrazolyl)borate) was combined with several hydroxypyridinone, hydroxypyridinethione, pyrone, and thiopyrone ligands to form the corresponding [(Tp(Ph,Me))Co(L)] complexes. X-ray crystal structures of these complexes were obtained to determine the mode of binding for each ligand L. The structures show that the [(Tp(Ph,Me))Co(L)] complexes are pentacoordinate complexes, with a general tendency toward square pyramidal geometry. The electronic, EPR, and paramagnetic NMR spectroscopy of the [(Tp(Ph,Me))Co(L)] complexes have been examined. The frozen-solution EPR spectra are indicative of pentacoordination in frozen solution, while the NMR indicates some dynamics in ligand binding. The findings presented here suggest that [(Tp(Ph,Me))Co(L)] complexes can be used as spectroscopic references for investigating the mode of inhibitor binding in metalloproteinases of medicinal interest. Potential limitations when using cobalt(II) model complexes are also discussed.     

A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors

As of mid-2017, only one structure of the human immunodeficiency virus (HIV) integrase core domain co-crystallised with an active site inhibitor was reported. In this structure (1QS4), integrase is complexed with a diketo-acid based strand-transfer inhibitor (INSTI). This structure has been a preferred platform for the structure-based design of INSTIs despite concerns relating to structural irregularities arising from crystallographic packing effects. A survey of the current pool of 297 reported integrase catalytic core structures indicated that the anatomy of the active site in the complex structure 1QS4 exhibits subtle variations relative to all other structures examined. Consequently, the 1QS4 structure was employed for docking studies. From the docking of twenty-seven allyltyrosine analogues, a 3-point inhibitor binding motif required for activity was established and successfully utilised in the development of a tripeptide displaying an EC₅₀ value of 10 ± 5 μM in HIV infected human T-cells. Additional docking of “in-house” compound libraries unearthed a methyl ester based nitrile derivative displaying an IC₅₀ value of 0.5 μM in a combined 3′-processing and strand-transfer assay.     

An approach to computer-aided inhibitor design: Application to cathepsin L

Summary We have developed an approach to search for molecules that can be used as lead compounds in designing an inhibitor for a given proteolytic enzyme when the 3D structure of a homologous protein is known. This approach is based on taking the cast of the binding pocket of the protease and comparing its dimensions with that of the dimensions of small molecules. Herein the 3D structure of papain is used to model cathepsin L using the comparative modeling technique. The cast of the binding pocket is computed using the crystal structure of papain because the structures of papain and the model of cathepsin L are found to be similar at the binding site. The dimensions of the cast of the binding site of papain are used to screen for molecules from the Cambridge Structural Database (CSD) of small molecules. Twenty molecules out of the 80 000 small molecules in the CSD are found to have dimensions that are accommodated by the papain binding pocket. Visual comparison of the shapes of the cast and the 20 screened molecules resulted in identifying brevotoxin b, a toxin isolated from the red tide dinoflagellate Ptycho brevis (previously classified as Gymonodium breve), as the structure that best fits the binding pocket of papain. We tested the proteolytic activity of papain and cathepsin L in the presence of brevotoxin b and found inhibition of papain and cathepsin L with K_is of 25 M and 0.6 M, respectively. We also compare our method with a more elaborate method in the literature, by presenting our results on the computer search for inhibitors of the HIV-1 protease.     

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays

We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors.     

A rational approach to the design and synthesis of chiral organopalladium-amine complexes

A new chiral auxiliary, (+/-)-N,N-dimethyl-1-(2,5-dimethylphenyl)ethylamine, was designed and synthesized in two steps from 1-acetyl-2,5-dimethylbenzene. Its cyclopalladated dimeric complex could be efficiently resolved via the formation of (S)-prolinate derivatives. Both hand forms of the complex could be obtained in similar yields. Despite the enormous inter-chelate steric constraints, the bulky monodentate ligand 3,4-dimethyl-1-phenylphosphole (DMPP) is able to coordinate regiospecifically to the orthopalladated 2,5-dimethylbenzylamine unit trans to the NMe(2) group. Compared to its naphthylamine analogue, the orthopalladated 2,5-dimethylbenzylamine complex exhibits a significantly higher stereoselectivity in the chiral template promoted asymmetric cycloaddition reaction between DMPP and ethyl vinyl ketone.     

Theoretical calculation and prediction for experimental design to obtain spin crossover complexes

DFT methods were utilized to study SCO complexes. [Fe(2btz)₂(NCX)₂] (2btz = 2,2′‐bithiazoline, X = S ( 1 ) and Se ( 2 )), [Fe(phen)₂(NCX)₂] (phen = 1,10‐phenantroline, X = S ( 3 ) and Se ( 4 )), and [Fe(bpy)₂(NCS)₂] ( 5 ) (bpy = 2,2′‐bipyridine) compounds, which have experimentally shown SCO behavior, were calculated. B3LYP, B3LYP*, OPBE, and OLYP with 6‐31G* and 6‐311 + G** basis sets were employed to calculate the ΔE_HS/LS energy gap as a clue to find complexes with SCO behavior. It is found that calculated result by B3LYP* with c₃ = 0.14 and OPBE methods and 6‐31G* basis set are in agreement with experimentally observed SCO complexes. Then, newly designed Fe(N‐N)₂(X)₂ complexes, where N‐N are bidentate nitrogen donor chelating ligands and X= SCN^‐, SeCN^‐, Cl^‐, Br^‐, I^‐, were chosen to see their potential to be SCO compounds. ΔE_HS/LS for potential SCO complexes are estimated from 0.8 to 6.5 kcal/mol in B3LYP* and 0.6–5.7 kcal/mol in OPBE. These calculations suggest [Fe(bpy)₂(NCSe)₂], [Fe(5dmbpy)₂(NCS)₂], and [Fe(3‐BrPhen)₂(NCSe)₂] compounds have the ability to show SCO behavior. © 2016 Wiley Periodicals, Inc.     

Using Tc-Re chemical analogy to synthesize and identify new99mTc complexes

The strong chemical resemblance between Tc and Re is applied to design and evaluate experiments with^99mTc complexes. A combination of spectrophotometric and electrophoretic techniques allows to propose the formula [TcO₂/amine/₂]⁺ for compounds prepared by reduction of^99mTcO ₄ ^– with Zn /solid phase/ in presence of several /bidentate/ amines.     

Using oxidative crosslinking and proximity labeling to quantitatively characterize protein-protein and protein-Peptide complexes

The quantitative analysis of protein-protein and protein-peptide complexes is of fundamental importance in biochemistry. We report here that nickel-catalyzed proximity biotinylation and Ru(II)(bpy)(3)(2+)-mediated oxidative crosslinking can be used to measure the equilibrium dissociation constant and stoichiometry of protein complexes. Only small amounts of protein are required, neither of the binding partners must be immobilized on a surface, and no special instrumentation is necessary. This chemistry should provide a useful complement to existing methods for the analysis of protein-protein and protein-peptide interactions.     

Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Using mesoscopic models to design strong and tough biomimetic polymer networks

Using computational modeling, we investigate the mechanical properties of polymeric materials composed of coiled chains, or "globules", which encompass a folded secondary structure and are cross-linked by labile bonds to form a macroscopic network. In the presence of an applied force, the globules can unfold into linear chains and thereby dissipate energy as the network is deformed; the latter attribute can contribute to the toughness of the material. Our goal is to determine how to tailor the labile intra- and intermolecular bonds within the network to produce material exhibiting both toughness and strength. Herein, we use the lattice spring model (LSM) to simulate the globules and the cross-linked network. We also utilize our modified Hierarchical Bell model (MHBM) to simulate the rupture and reforming of N parallel bonds. By applying a tensile deformation, we demonstrate that the mechanical properties of the system are sensitive to the values of N(in) and N(out), the respective values of N for the intra- and intermolecular bonds. We find that the strength of the material is mainly controlled by the value of N(out), with the higher value of N(out) providing a stronger material. We also find that, if N(in) is smaller than N(out), the globules can unfold under the tensile load before the sample fractures and, in this manner, can increase the ductility of the sample. Our results provide effective strategies for exploiting relatively weak, labile interactions (e.g., hydrogen bonding or the thiol/disulfide exchange reaction) in both the intra- and intermolecular bonds to tailor the macroscopic performance of the materials.     

Using Gaussian model to improve biological sequence comparison

One of the major tasks in biological sequence analysis is to compare biological sequences, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Numerous efficient methods have been developed for sequence comparison, but challenges remain. In this article, we proposed a novel method to compare biological sequences based on Gaussian model. Instead of comparing the frequencies of k‐words in biological sequences directly, we considered the k‐word frequency distribution under Gaussian model which gives the different expression levels of k‐words. The proposed method was tested by similarity search, evaluation on functionally related genes, and phylogenetic analysis. The performance of our method was further compared with alignment‐based and alignment‐free methods. The results demonstrate that Gaussian model provides more information about k‐word frequencies and improves the efficiency of sequence comparison. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Rational design of multi-targeting ruthenium- and platinum-based anticancer complexes

Platinum-based anticancer drugs, including cisplatin and its analogues, have played important roles in the clinical treatment of solid tumors over the past 38 years. However, poor selectivity, high toxicity and intrinsic or acquired drug resistance profoundly limit their application, which encourages the development of novel transition metal-based anticancer agents with different mechanisms of action. To this end, transition metal complexes that can simultaneously act on more than one target, termed as single-molecule multi-targeting complexes, have attracted increasing attention because of their enhanced efficacy and diminished chance of drug resistance. In this review, we systematically discuss the recent progress in the development of platinum- and ruthenium-based anticancer agents, in particular the rational design of platinum and ruthenium complexes with multi-targeting features.     

Using ligand bite angles to control the hydricity of palladium diphosphine complexes

A series of [Pd(diphosphine)(2)](BF(4))(2) and Pd(diphosphine)(2) complexes have been prepared for which the natural bite angle of the diphosphine ligand varies from 78 degrees to 111 degrees. Structural studies have been completed for 7 of the 10 new complexes described. These structural studies indicate that the dihedral angle between the two planes formed by the two phosphorus atoms of the diphosphine ligands and palladium increases by over 50 degrees as the natural bite angle increases for the [Pd(diphosphine)(2)](BF(4))(2) complexes. The dihedral angle for the Pd(diphosphine)(2) complexes varies less than 10 degrees for the same range of natural bite angles. Equilibrium reactions of the Pd(diphosphine)(2) complexes with protonated bases to form the corresponding [HPd(diphosphine)(2)](+) complexes were used to determine the pK(a) values of the corresponding hydrides. Cyclic voltammetry studies of the [Pd(diphosphine)(2)](BF(4))(2) complexes were used to determine the half-wave potentials of the Pd(II/I) and Pd(I/0) couples. Thermochemical cycles, half-wave potentials, and measured pK(a) values were used to determine both the homolytic ([HPd(diphosphine)(2)](+) --> [Pd(diphosphine)(2)](+) + H*) and the heterolytic ([HPd(diphosphine)(2)](+) --> [Pd(diphosphine)(2)](2+) + H(-)) bond-dissociation free energies, Delta G(H*)* and Delta G(H-)*, respectively. Linear free-energy relationships are observed between pK(a) and the Pd(I/0) couple and between Delta G(H-)* and the Pd(II/I) couple. The measured values for Delta G(H*)* were all 57 kcal/mol, whereas the values of Delta G(H-)* ranged from 43 kcal/mol for [HPd(depe)(2)](+) (where depe is bis(diethylphosphino)ethane) to 70 kcal/mol for [HPd(EtXantphos)(2)](+) (where EtXantphos is 9,9-dimethyl-4,5-bis(diethylphosphino)xanthene). It is estimated that the natural bite angle of the ligand contributes approximately 20 kcal/mol to the observed difference of 27 kcal/mol for Delta G(H-)*.     

Surface active macromolecular and supramolecular complexes: design and catalysis

A number of macromolecular and supramolecular catalysts which combine the functions of transition metal complex, phase transfer agent with molecular recognition ability has been designed. The complexes of rhodium, palladium, iron and copper showed the remarkable activity in hydroformylation, Wacker‐type oxidation of various olefins, oxidation of alkanes and hydroxylation of aromatics.     

Using molecular dynamics and quantum mechanics calculations to model fluorescence observables

We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the independent snapshot method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments.     

Comparison of the shape parameters of DNA-cationic lipid complexes and model polyelectrolyte-lipid complexes

In this study, we used a rheological method to study the shape of DNA-cationic lipid complexes and model polyelectrolyte-lipid complexes. We introduced two kinds of anionic polyelectrolytes, sodium polygalacturonate (PGU) and sodium dextran sulfate (DSS), of varying size, as models for DNA. The prepared complexes were incubated under laminar flow conditions. The results show the same quantitative relation between the shape parameter of lipoplexes and the length of anionic polyelectrolytes, including DNA. The rheological behavior of PGU and DSS were similar to that of DNA.     

Using Monte Carlo simulations and self-consistent field theory to design interfacially active copolymers

We use both Monte Carlo computer simulations and numerical self-consistent field lattice calculations to determine the behavior of copolymers at penetrable and impenetrable interfaces. These computational techniques are useful as “design tools”: they allow us to systemically vary the copolymer architecture, determine optimal structures for specific applications, and establish guidelines for fabricating copolymers that yield the desired interfacial properties. We illustrate this principle with three different examples. In the first study, we combine the techniques to design copolymer compatibilizers that enhance the strength of immiscible polymer blends. These copolymers contain teeth that associate across the penetrable interface between the phase-separated regions and form a “molecular velcro” that effectively binds the regions together. In the case of impenetrable interfaces, we determine how the copolymer sequence distribution affects the structure of a layer of copolymers grafted onto a solid surface. The results indicate how to control the morphology of the layer and the surface properties of the substrate, by varying the microstructure of the grafted copolymers. Finally, we design a polymer channel that “opens” and “closes” in response to changes in the pH and quality of the surrounding solvent. The channel is formed from polyacid chains that are anchored onto a solid surface. Due to these properties, the system can be used for controlled release or sensor devices.