Search results for "Rational design"

Hyaluronic acid dressing of Hydrophobic Carbon Nanodots: a Self-assembling Strategy of Hybrid Nanocomposites with Theranostic Potential

2021

We propose a rational design of hyaluronic acid-dressed red-emissive carbon dots (CDs), with a well-structured hydrophobic core capable of locally delivering high amount doxorubicin (Doxo) (> 9% w/w) and heat (hyperthermia) in a light stimuli sensitive fashion. We combined in a unique micelle-like superstructure the peculiar optical properties of CDs (NIR photothermal conversion and red fluorescence) with the ability of hyaluronic acid (HA) shell of stabilizing nanomedicines in aqueous environment and recognizing cancer cells overexpressing CD44 receptors on their membranes, thus giving rise to smart theranostic agents useful in cancer imaging and NIR-triggered chemo-phototherapy of solid t…

Immunoproteasome and Non-Covalent Inhibition: Exploration by Advanced Molecular Dynamics and Docking Methods

2021

The selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune, inflammatory diseases, and hematologic malignancies. Recently, a new series of amide derivatives as non-covalent inhibitors of the β1i subunit with Ki values in the low/submicromolar ranges have been identified. Here, we investigated the binding mechanism of the most potent and selective inhibitor, N-benzyl-2-(2-oxopyridin-1(2H)-yl)propanamide (1), to elucidate the steps from the ligand entrance into the binding pocket to the ligand-induced conformational changes. We carried out a total of 400 ns of MD-binding analyses, followed by 200 ns of plain MD. The trajectories clustering allowed identifying thre…

Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations

2011

The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary …

Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.

2016

We propose a structure-based protocol for the development of customized covalent inhibitors. Starting from a known inhibitor, in the first and second steps appropriate substituents of the warhead are selected on the basis of quantum mechanical (QM) computations and hybrid approaches combining QM with molecular mechanics (QM/MM). In the third step the recognition unit is optimized using docking approaches for the noncovalent complex. These predictions are finally verified by QM/MM or molecular dynamic simulations. The applicability of our approach is successfully demonstrated by the design of reversible covalent vinylsulfone-based inhibitors for rhodesain. The examples show that our approach…

Rational design, tailored synthesis and characterisation of ordered mesoporous silicas in the micron and submicron size range

2000

Immunoassays for trifloxystrobin analysis. Part I. Rational design of regioisomeric haptens and production of monoclonal antibodies

2014

Trifloxystrobin is one of the main active principles belonging to the strobilurin family of crop protection compounds. In this article, the synthesis of a battery of regioisomeric functionalized derivatives of trifloxystrobin is described. The same aliphatic linear carboxylated chain was introduced as spacer arm in all of the synthesized haptens, but it was located at different positions of the parent molecule. N,N′-Disuccinimidyl carbonate was employed for hapten activation, so the resulting N-hydroxysuccinimyl ester could be readily purified and efficiently coupled to proteins. After immunization and hybridoma generation, a collection of 20 mouse monoclonal antibodies from different immun…

Engineering of chicken avidin: a progressive series of reduced charge mutants.

1998

Avidin, a positively charged egg-white glycoprotein, is a widely used tool in biotechnological applications because of its ability to bind biotin strongly. The high pI of avidin (approximately 10.5), however, is a hindrance in certain applications due to non-specific (charge-related) binding. Here we report a construction of a series of avidin charge mutants with pIs ranging from 9.4 to 4.7. Rational design of the avidin mutants was based on known crystallographic data together with comparative sequence alignment of avidin, streptavidin and a set of avidin-related genes which occur in the chicken genome. All charge mutants retained the ability to bind biotin tightly according to optical bio…

Decisive influence of substitution positions in molecular self-assembly

2014

Molecular self-assembly provides a versatile tool for creating functional molecular structures at surfaces. A rational design of molecular structure formation requires not only an in-depth understanding of the subtle balance between intermolecular and molecule-surface interactions, but might also involve considering chemical changes of the molecules, such as deprotonation. Here, we present a systematic investigation of a comparatively simple class of molecules, namely dihydroxybenzoic acid, which, nevertheless, enables creating a rich variety of structures when deposited onto calcite (10.4) held at room temperature. Based on non-contact atomic force microscopy measurements in ultra-high vac…

What Is Synthetic Biology?

2014

Synthetic biology aims at the design and construction of biological devices and systems for useful purposes. From an ideal engineering perspective synthetic biology works from rational design made through a few conceptual pillars, namely abstraction, standardization and modularity. Nevertheless, the combination of our still fragmentary biological knowledge and the messy nature of biological devices are major challenges for engineering life in a predictive manner. It is urgent to build bridges between different disciplines, from biology to engineer and back, to pursue this extraordinary goal of making life.

Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel

2020

Fructosyl peptide oxidases (FPOXs) are enzymes currently used in enzymatic assays to measure the concentration of glycated hemoglobin and albumin in blood samples, which serve as biomarkers of diabetes. However, since FPOX are unable to work directly on glycated proteins, current enzymatic assays are based on a preliminary proteolytic digestion of the target proteins. Herein, to improve the speed and costs of the enzymatic assays for diabetes testing, we applied a rational design approach to engineer a novel enzyme with a wider access tunnel to the catalytic site, using a combination of Rosetta design and molecular dynamics simulations. Our final design, L3_35A, shows a significantly wider …