Computer-aided drug design,quantum-mechanical methods for biological problems

Quantum chemistry enables to study systems with chemical accuracy (<1 kcal/mol from experiment) but is restricted to a handful of atoms due to its computational expense. This has led to ongoing interest to optimize and simplify these methods while retaining accuracy. Implementing quantum mechanical (QM) methods on modern hardware such as multiple-GPUs is one example of how the field is optimizing performance. Multiscale approaches like the so-called QM/molecular mechanical method are gaining popularity in drug discovery because they focus the application of QM methods on the region of choice (e.g., the binding site), while using efficient MM models to represent less relevant areas. The creation of simplified QM methods is another example, including the use of machine learning to create ultra-fast and accurate QM models. Herein, we summarize recent advancements in the development of optimized QM methods that enhance our ability to use these methods in computer aided drug discovery.     

Computer-aided design, synthesis and biological assay of p-methylsulfonamido phenylethylamine analogues

Class III antiarrhythmic agents selectively delay the effective refractory period (ERP) and increase the transmembrance action potential duration (APD). Based on our previous studies, a set of 17 methylsulfonamido phenylethylamine analogues were investigated by 3D-QSAR techniques of CoMFA and CoMSIA. The 3D-QSAR models proved a good predictive ability, and could describe the steric, electrostatic and hydrophobic requirements for recognition forces of the receptor site. According to the clues provided by this 3D-QSAR analysis, we designed and synthesized a series of new analogues of methanesulfonamido phenylethylamine (VIa-i). Pharmacological assay indicated that the effective concentrations of delaying the functional refractory period (FRP) 10ms of these new compounds have a good correlation with the 3D-QSAR predicted values. It is remarkable that the maximal percent change of delaying FRP in microM of compound VIc is much higher than that of dofetilide. The results showed that the 3D-QSAR models are reliable.     

Toward scalable parts families for predictable design of biological circuits

Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.     

Computer-aided gene design.

A computer program, which runs on MS-DOS personal computers, is described that assists in the design of synthetic genes coding for proteins. The goal of the program is the design of a gene which (i) contains as many unique restriction sites as possible and (ii) uses a specific codon usage. The gene designed according to the criteria above is (i) suitable for 'modular mutagenesis' experiments and (ii) optimized for expression. The program 'reverse-translates' protein sequences into degenerated DNA sequences, generates a map of potential restriction sites and locates sequence positions where unique restriction sites can be accommodated. The nucleic acid sequence is then 'refined' according to a specific codon usage to remove any degeneration. Unique restriction sites, if potentially present, can be 'forced' into the degenerated nucleic acid sequence by using 'priority codes' assigned to different restriction sequences.     

Computer-aided design in protein engineering

The amino acid sequence of a protein can be engineered genetically to yield a molecule with modified or novel properties of clinical or industrial importance, through knowledge of the relationships between sequence, three-dimensional structure and function. Interactive computer graphics can display and model the structural information revealed by protein cyrstallography. In the absence of a suitable crystal structure, computer methods must predict protein conformation from sequence. The most powerful approaches for structure prediction are based on sequence homology or a more general analogy with known crystal structures. Improvements in these methods will require access to data bases containing the basic motifs of protein architecture.     

Dynamical roles of biological regulatory circuits

Regulatory circuits are found at the basis of all non-trivial dynamical properties of biological networks. More specifically, positive circuits are involved in the generation of multiple differentiated states, whereas negative circuits can generate cyclic or homeostatic behaviours. These notions are briefly reviewed, from initial biological formulations to mathematical formalisations, further encompassing their application to the design of synthetic regulatory systems. Finally, current challenges for the analysis of increasingly complex regulatory networks are indicated, as well as prospects for our understanding of development and evolution.     

Computer-aided model-building strategies for protein design

Model-building strategies for protein modification and design are developed. These strategies emphasize simple geometric aspects of protein structure, use local coordinate systems defined at particular residues, and systematically consider a large number of alternative sequences and conformations. We have written a computer program, PROTEUS, to implement these search methods. PROTEUS has been used to find positions where disulfide bonds could be added to the N-terminal domain of the lambda repressor and to predict how a loop on the surface of repressor could be shortened.     

Computer-aided design of novel siderophores: pyridinochelin

Pyridinochelin, a novel tetradentate catecholate-type siderophore, has been designed on the basis of the active analog enterobactin and was then synthesized. Growth promotion tests indicate that this synthetic siderophore feeds various pathogenic bacteria most effectively with iron even though it lacks one catecholate group compared to enterobactin. The superposition of the mentioned siderophore structures suggests that the structure of the skeleton connecting the catecholate groups might be an important factor for the iron transport.     

Computer-aided design of polyketides with the required properties

An approach to rational design of new polyketides with the required spectrum of biological activity has been proposed. We have developed the BioGenPharm software, which generates combinatorial libraries of polyketides based on the user-defined input parameters, performs prediction of biological activity spectra for the generated structures and selection of molecuels with the required properties. PASS algorithm has been applied for prediction of polyketide activity spectra (http://www.ibmc.msk.ru/PASS). Validation of PASS prediction ability for polyketides was performed vs. the evaluation set containing 242 natural macrolides from the Dictionary of Natural Products. The mean prediction accuracy was 75.5%. The problem of choice of the cutting points for probability of the presence of activity (Pa), which provides optimal combination of such parameters as sensitivity, specificity, concordance has been considered. Applicability of the described method has been illustrated by generation of a virtual library of the erythromycin analogues and selection of substances with low probability of the hepatotoxic effect.     

Synthetic genetic circuits for programmable biological functionalities

Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.     

Coded-exposure camera and its circuits design

In the industrial production line, the motion of the target is the main reason for blurred image of the camera monitoring. A coded-exposure devices and circuits are designed to get restored image from this motion blurring. A given binary code sequence which represent open or close of shutter in CCD circuits driven by FPGA is used to control the exposure-time. The sampled images are processed by deconvolution algorithm and the high frequency information of them could be preserved by using the coded-exposure sequence resulting in blurred image restoration. The de-blurred problem could be converted to a well-posed from an ill-posed one. Experiments demonstrate that using the coded-exposure, the device proposed is able to improve the quality of blurred image.     

Computer-aided design and manufacture of an above-knee amputee socket

This paper describes the initial test results obtained from a newly developed computer-aided socket design (CASD) and manufacturing (CASM) process for above-knee amputees. Anthropometric measures taken from an amputee provided input information to a CASD system. Using these measurements, data from a reference shape library stored in the computer were selected and modified to create a unique socket shape reflecting the particular characteristics of the amputation stump. The resultant shape was produced as a ‘primitive’ test socket by a CASM process. Numerical shape data were then transferred to a CNC milling machine to construct a negative cast, from which the primitive socket was produced by a vacuum-forming procedure. The resultant primitive socket shape was fitted and the amputee was able to load the socket without discomfort. Some shape discrepancies were identified and the shape data were modified interactively by the CASD system to create a final socket shape. The final socket shape was manufactured and worn by the amputee during a 35 min walking trial. Subjective evaluation was that the socket provided comfort and control comparable with that of the conventional socket, and proved to be acceptable to the amputee. This was followed by a 2-month home trial which was also successful. The CASD socket shapes were compared numerically in area, shape and volume with data taken from the original socket worn by the amputee, a new socket made by conventional methods and a topographic model of the amputation stump. The final CASD socket shape compared favourably with that of a socket manufactured by conventional methods. Results indicated that by the use of the CASD/CASM process, it was possible to produce an above-knee prosthetic socket which provided comfort and control for the amputee.     

Automatic design of digital synthetic gene circuits

De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.     

Computer-aided dental prostheses construction using reverse engineering

The implementation of computer-aided design/computer-aided manufacturing (CAD/CAM) systems with virtual articulators, which take into account the kinematics, constitutes a breakthrough in the construction of customised dental prostheses. This paper presents a multidisciplinary protocol involving CAM techniques to produce dental prostheses. This protocol includes a step-by-step procedure using innovative reverse engineering technologies to transform completely virtual design processes into customised prostheses. A special emphasis is placed on a novel method that permits a virtual location of the models. The complete workflow includes the optical scanning of the patient, the use of reverse engineering software and, if necessary, the use of rapid prototyping to produce CAD temporary prostheses.     

Computer-aided drug design: getting the best results.

There are two major stages in the design of drug molecules: lead-molecule development and lead-molecule optimization. Whereas a variety of computational chemistry and molecular modeling (CC/MM) techniques are now routinely and successfully applied to the optimization stage of drug design, the generation of initial lead compounds has proven a more difficult problem for the CC/MM approach. Only recently has the design of lead molecules by this route become a subject of active research. This article looks at the factors which must be considered carefully when incorporating CC/MM methods into different aspects of drug-design strategies.     

Computer-aided molecular design of pyrazolotriazines targeting glycogen synthase kinase 3

Numerous studies have highlighted the implications of the glycogen synthase kinase 3 (GSK-3) in several processes associated with Alzheimer’s disease (AD). Therefore, GSK-3 has become a crucial therapeutic target for the treatment of this neurodegenerative disorder. Hereby, we report the design and multistep synthesis of ethyl 4-oxo-pyrazolo[4,3-d][1–3]triazine-7-carboxylates and their biological evaluation as GSK-3 inhibitors. Molecular modelling studies allow us to develop this new scaffold optimising the chemical structure. Potential binding mode determination in the enzyme and the analysis of the key features in the catalytic site are also described. Furthermore, the ability of pyrazolotriazinones to cross the blood–brain barrier (BBB) was evaluated by passive diffusion and those who showed great GSK-3 inhibition and permeation to the central nervous system (CNS) showed neuroprotective properties against tau hyperphosphorylation in a cell-based model. These new brain permeable pyrazolotriazinones may be used for key in vivo studies and may be considered as new leads for further optimisation for the treatment of AD.