Rational design of an enzyme mutant for anti-cocaine therapeutics

(-)-Cocaine is a widely abused drug and there is no available anti-cocaine therapeutic. The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority. An ideal anti-cocaine medication would be to accelerate (-)-cocaine metabolism producing biologically inactive metabolites. The main metabolic pathway of cocaine in body is the hydrolysis at its benzoyl ester group. Reviewed in this article is the state-of-the-art computational design of high-activity mutants of human butyrylcholinesterase (BChE) against (-)-cocaine. The computational design of BChE mutants have been based on not only the structure of the enzyme, but also the detailed catalytic mechanisms for BChE-catalyzed hydrolysis of (-)-cocaine and (+)-cocaine. Computational studies of the detailed catalytic mechanisms and the structure-and-mechanism-based computational design have been carried out through the combined use of a variety of state-of-the-art techniques of molecular modeling. By using the computational insights into the catalytic mechanisms, a recently developed unique computational design strategy based on the simulation of the rate-determining transition state has been employed to design high-activity mutants of human BChE for hydrolysis of (-)-cocaine, leading to the exciting discovery of BChE mutants with a considerably improved catalytic efficiency against (-)-cocaine. One of the discovered BChE mutants (i.e., A199S/S287G/A328W/Y332G) has a approximately 456-fold improved catalytic efficiency against (-)-cocaine. The encouraging outcome of the computational design and discovery effort demonstrates that the unique computational design approach based on the transition-state simulation is promising for rational enzyme redesign and drug discovery.     

Rational design of nanocarriers for mitochondria-targeted drug delivery

Well-developed mitochondria-targeted nanocarriers for function regulation are highly desirable. Numerous studies have been conducted on the treatment of mitochondria-related diseases; however, further improvements are required to develop more effective drug delivery methods. Herein, we comprehensively introduce recent developments progress in rational design of mitochondria-targeted nanocarriers, and discuss the different strategies of available nanocarriers for targeting mitochondria. We also highlight the advantages and disadvantages of various carrier systems that are currently in use. Finally, perspective on new generation for mitochondria-targeted delivery systems in the emerging area of drug-based therapeutics is also discussed.     

Rational design of a macrocycle-based chemosensor for anions

A macrocycle-based fluorescence chemosensor has been designed and synthesized from the reaction of dansyl chloride and a hexaaminomacrocycle containing four secondary and two tertiary amines. The new chemosensor has been examined for its binding ability towards phosphate, sulfate, nitrate, iodide, bromide, chloride, and fluoride by fluorescence spectroscopy in DMSO. The results indicate that the compound binds each of the anions with a 1:1 stoichiometry, showing high affinity for oxoanions, chloride, and iodide with binding constants up to four orders of magnitude. Ab initio calculations based on density functional theory (DFT) suggest that the ligand is deformed in order to encapsulate an anion, and each anion, except fluoride, is bonded to the macrocycle through two NH?X⁻ and four CH?X⁻ interactions.     

Rational design of cavitand receptors for mass sensors

This Communication describes a rational approach to the fabrication of selective mass sensors, using multiple hydrogen-bonding type interactions encoded in a single cavitand receptor. The introduction of two inward facing hydrogen bond acceptor PO groups at the upper rim of a cavitand renders the corresponding receptor layer deposited on a mass transducer highly selective toward alcohol vapors. The molecular origin of the increased selectivity has been identified in the presence of two energetically and geometrically equivalent interaction modes available to the guest, giving to the corresponding complexes an entropic advantage over their mono PO analogues.     

Rational design of iridium–porphyrin conjugates for novel synergistic photodynamic and photothermal therapy anticancer agents

Near-infrared (NIR) emitters are important probes for biomedical applications. Nanoparticles (NPs) incorporating mono- and tetranuclear iridium(iii) complexes attached to a porphyrin core have been synthesized. They possess deep-red absorbance, long-wavelength excitation (635 nm) and NIR emission (720 nm). TD-DFT calculations demonstrate that the iridium–porphyrin conjugates herein combine the respective advantages of small organic molecules and transition metal complexes as photosensitizers (PSs): (i) the conjugates retain the long-wavelength excitation and NIR emission of porphyrin itself; (ii) the conjugates possess highly effective intersystem crossing (ISC) to obtain a considerably more long-lived triplet photoexcited state. These photoexcited states do not have the usual radiative behavior of phosphorescent Ir(iii) complexes, and they play a very important role in promoting the singlet oxygen (¹O₂) and heat generation required for photodynamic therapy (PDT) and photothermal therapy (PTT). The tetranuclear 4-Ir NPs exhibit high ¹O₂ generation ability, outstanding photothermal conversion efficiency (49.5%), good biocompatibility, low half-maximal inhibitory concentration (IC₅₀) (0.057 μM), excellent photothermal imaging and synergistic PDT and PTT under 635 nm laser irradiation. To our knowledge this is the first example of iridium–porphyrin conjugates as PSs for photothermal imaging-guided synergistic PDT and PTT treatment in vivo.

Iridium–porphyrin conjugates assembled in nanoparticles are photosensitizers that exhibit excellent photothermal imaging and synergistic PDT and PTT in vivo.     

Rational design of allosteric ribozymes

Background: Efficient operation of cellular processes relies on the strict control that each cell exerts over its metabolic pathways. Some protein enzymes are subject to allosteric regulation, in which binding sites located apart from the enzyme's active site can specifically recognize effector molecules and alter the catalytic rate of the enzyme via conformational changes. Although RNA also performs chemical reactions, no ribozymes are known to operate as true allosteric enzymes in biological systems. It has recently been established that small-molecule receptors can readily be made of RNA, as demonstrated by the in vitro selection of various RNA aptamers that can specifically bind corresponding ligand molecules. We set out to examine whether the catalytic activity of an existing ribozyme could be brought under the control of an effector molecule by designing conjoined aptamer-ribozyme complexes.Results: By joining an ATP-binding RNA to a self-cleaving ribozyme, we have created the first example of an allosteric ribozyme that has a catalytic rate that can be controlled by ATP. A 180-fold reduction in rate is observed upon addition of either adenosine or ATP, but no inhibition is detected in the presence of dATP or other nucleoside triphosphates. Mutations in the aptamer domain that are expected to eliminate ATP binding or that increase the distance between aptamer and ribozyme domains result in a loss of ATP-specific allosteric control. Using a similar design approach, allosteric hammerhead ribozymes that are activated in the presence of ATP were created and another ribozyme that can be controlled by theophylline was created.Conclusions: The catalytic features of these conjoined aptamer-ribozyme constructs demonstrate that catalytic RNAs can also be subject to allosteric regulation — a key feature of certain protein enzymes. Moreover, by using simple rational design strategies, it is now possible to engineer new catalytic polynucleotides which have rates that can be tightly and specifically controlled by small effector molecules.     

Rational design of porous titanophosphates

To rationally design new nanoporous materials based on titanophosphates, a small library of titanium phosphate crystalline nanoporous compounds has been build up and its compounds have been investigated by X-ray diffraction and by in- and ex-situ NMR. The main trends of the unusual titanium solution chemistry, of the prenucleation building units and of their assembling have been established. The classical trial and error strategy can therefore be replaced by a better control of the steps leading to the final targeted network.     

Rational design of DNA nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.     

Rational design of polymer colloids

Recent advances in understanding of the fundamental mechanistic events in emulsion polymerization give the potential for rational design of new materials based on polymer colloids. It is now possible to design a new industrial process from first principles, based on well‐understood mechanistic principles. An overview of recent developments in the fundamental science of emulsion polymerization is given, with examples of the application of this knowledge to topologically‐controlled synthesis of novel materials based on natural rubber and polybutadiene seed latexes.     

Rational principles of compound selection for combinatorial library design

It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.     

Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations

Combined docking and molecular dynamics (MD) simulations are carried out for the rational design of affinity peptide ligand of tissue-type plasminogen activator (t-PA). Ten amino acids that have high affinity to three different regions of t-PA are identified by the amino acids location method on the basis of candidate pocket structure of t-PA. Then, 14 tetrapeptides are built and docked into the candidate pocket of t-PA. The absolute value of the D(score) calculated from the docking simulation is used to assess the affinity of a peptide for t-PA. Consequently, six tetrapeptides that have high D(score) values are selected and linked to a spacer arm of [NH(CH(2))(6)NH(2)] that is present on EAH Sepharose gel. The linked compounds are further evaluated by docking into the candidate pocket of t-PA. As a result, the tetrapeptide QDES with the highest D(score) value is selected. Molecular surface analysis with the MOLCAD program reveals that electrostatic interactions and hydrogen bonds (H-bonds) contribute to the affinity interactions between the tetrapeptide and t-PA. MD simulations indicate that QDES-t-PA complex keeps stable, and the distances between the carboxyl groups of Asp189, Gln192 and Asp194 and the charged amino group of glutamine change little. Moreover, all the nine H-bonds found in the docking simulation are confirmed by the MD simulations. It is also found that three water molecules act as bridges between the ligand and the protein pocket by hydrogen bonding. Finally, high binding affinity and specificity of the peptide ligand are confirmed by the purification of t-PA from crude porcine heart extract using the immobilized-ligand column for affinity chromatography.     

Rational design of platinum-group-metal-free electrocatalysts for oxygen reduction reaction

Platinum-group-metal (PGM)-free materials have been promised as potential replacement for Pt as the cathodic catalyst in proton exchange membrane fuel cells. Critical design criteria of the PGM-free catalyst reside on the high active site density to compensate its generally lower turn-over frequency and improved mass-charge transfers during the electrocatalysis. This short review summarizes the research activities in recent years from our team at Argonne National Laboratory in preparing highly active oxygen reduction reaction (ORR) catalysts using rationally designed porous organic precursors, as reported in the First Telluride Science Research Center (TSRC) Workshop on PGM-free Electrocatalysis in 2019. More recent studies by others are also discussed.     

Rational design of purification processes for recombinant proteins.

This paper discusses the elements important for rational design of purification processes for recombinant proteins. Main issues involved in selection of operations and process design are reviewed with particular emphasis on the challenges posed by recombinant proteins. This includes thermodynamic characterization of target protein and main contaminants, use of correlations and of expert knowledge for the development of an expert system for optimization and design (selection) of separation and purification (chromatographic) processes. The main deficiency in accurate information for rational process selection is in that required for high-resolution chromatographic processes. The authors show that a database with detailed information on properties of the main contaminants present in the fermentation streams of usual recombinant protein sources can be integrated to an expert system with an open architecture. This will allow more precise selection of unit operations for the design of protein purification processes.     

A novel method for enzyme design

Rational design of enzymes is a stringent test of our understanding of protein structure and function relationship, which also has numerous potential applications. We present a novel method for enzyme design that can find good candidate protein scaffolds in a protein-ligand database based on vector matching of key residues. Residues in the vicinity of the active site were also compared according to a similarity score between the scaffold protein and the target enzyme. Suitable scaffold proteins were selected, and the side chains of residues around the active sites were rebuilt using a previously developed side-chain packing program. Triose phosphate isomerase (TIM) was used as a validation test for enzyme design. Selected scaffold proteins were found to accommodate the enzyme active sites and successfully form a good transition state complex. This method overcomes the limitations of the current enzyme design methods that use limited number of protein scaffold and based on the position of ligands. As there are a large number of protein scaffolds available in the Protein Data Band, this method should be widely applicable for various types of enzyme design.     

Rational design of light-controllable polymer micelles

Amphiphilic block copolymer (BCP) micelles are nanocarriers that hold promise for controlled delivery applications. This account highlights our recent works on light-dissociable BCP micelles. We have designed and developed light-responsive amphiphilic BCPs whose micellar aggregates (core-shell micelles and vesicles) can be disrupted by light exposure. The basic strategy is to incorporate a chromophore into the structure of the hydrophobic block, whose photoreaction can result in a conformational or structural change that shifts the hydrophilic/hydrophobic balance toward the destabilization of the micelles. Using various chromophores including azobenzene, pyrene and nitrobenzene, we have achieved both reversible and irreversible dissociation of BCP micelles upon illumination with UV/visible or near infrared light. The demonstrated rational design principle based on light-changeable or light-switchable amphiphilicity is general and can be applied to many polymer/chromophore combinations. This opens the door to developing photocontrollable polymer nanocarriers offering control over when and where the release of loaded agents takes place.     

Rational design of a calcium-binding protein

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.     

Rational design of lanthanide binding peptides

Lanthanide-binding peptides are very attractive for the design of bioprobes. Indeed, they combine the amazing properties of lanthanide ions, such as their time-resolved luminescence (Eu, Tb) or electronic relaxation (Gd) to the characteristics of the peptide scaffold, such as large solubility in water and ability to recognize biological substrates. Peptides derived from natural amino acids are reviewed in a first section. Some of their lanthanide complexes have already demonstrated their efficiency in determining protein structures and functions. Then, we will show how insertion of chelating unnatural amino acids modulates peptide-lanthanide complexes properties, such as luminescence and stability.     

Rational design of chiral nanoscale adamantanoids

[formula: see text] Utilizing coordination as a motif, the self-organization of six ditopic and four tritopic building blocks leads to the formation of nanoscale adamantanoid frameworks.     

Rational drug design and high-throughput techniques for RNA targets

RNA molecules are the only known molecules which possess the double property of being depository of genetic information, like DNA, and of displaying catalytic activities, like protein enzymes. RNA molecules intervene in all steps of gene expression and in many other biological activities. Like proteins, RNAs achieve those biological functions by adopting intricate three-dimensional folds and architectures. Further, as in protein sequences, RNA sequences contain signatures specific for three-dimensional motifs which participate in recognition and binding. In regulatory pathways, RNA molecules exist in equilibria between transient structures differentially stabilized by effectors such as proteins or cofactors. Therefore, RNA molecules display their potential as drug targets on different levels, namely in three-dimensional folds, in structural equilibria and in RNA-protein interfaces. Several examples will be described together with the already available techniques for combinatorial synthesis and high-throughput screening of potential drug and target RNA molecules.     

Rational design of a reversible pH-responsive switch for peptide self-assembly

Peptide TZ1H, based on the heptad sequence of a coiled-coil trimer, undergoes fully reversible, pH-dependent self-assembly into long-aspect-ratio helical fibers. Substitution of isoleucine residues with histidine at the core d-positions of alternate heptads introduces a mechanism by which self-assembly is coupled to the protonation state of the imidazole side chain. Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.