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Topic Review
Commercial Targeted Libraries in Drug Design
After the identification of a biological target (enzyme, receptor, protein and so on), the focus of the early phase of drug discovery rests on the identification of leads or compounds that exhibit pharmacological activity against this specific target. Compounds of interest are most often discovered in pre-existing libraries of compounds that can be either virtual or physical. Computer-aided methods which have become increasingly important over the years in drug development utilize virtual compound libraries. While physical compound libraries reach the number of millions of molecules, virtual compound libraries created by large pharmaceutical companies can range from 107 to 1018 molecules. Investigations of these libraries identifies specific molecules, synthetic pathways and focus on a specific chemical space. Targeted libraries are often smaller and are focused towards a specific chemical space. They are created by using relevant biological information with the aim to decrease the processing time associated with larger libraries while maintaining the most relevant chemical space where lead compounds can be found. Due to the fact that they required less computational or wet-lab labor to process they have become very popular with smaller laboratories which try to compete in the drug-development sector. Many modern vendors of compounds today offer such libraries, but the quality of the procedure used to define desired chemical space and select compounds is questionable.
  • 1.3K
  • 25 May 2022
Topic Review
PAMAM Dendrimers
Poly(amidoamine) (PAMAM) dendrimers are repetitively branched, three-dimensional molecules, made of amide and amine subunits, possessing unique physiochemical properties.
  • 1.3K
  • 15 Feb 2022
Topic Review Peer Reviewed
The Applications of Microphysiological Systems in Biomedicine: Impact on Urologic and Orthopaedic Research
Microphysiological systems (MPSs) are in vitro models that can incorporate dynamic stimuli such as flow, pressure and contraction in cell culture, enabling the formation of cellular architectures and retrieving physiological function often absent in conventional 2D-cell culture. MPS applications saw a substantial growth in recent years, drawing attention from industry as a strategy to optimize pre-clinical drug-development purposes, as well as from biomedical research, to fill a gap between in vivo and in vitro models. Several MPS platforms are now available and are employed in the development of bone and kidney complex systems for urologic and orthopaedic research. These advances have enabled, for example, the in vitro modelling of bone regeneration and renal drug secretion, and have dramatic potential to improve research into both orthopaedic and urology cancers. 
  • 1.2K
  • 16 Jun 2022
Topic Review
Electrical Source Imaging
Electrical Source Imaging (ESI) is an imaging technique utilized to localize the activated brain regions by incorporating temporal and spatial components from electroencephalogram (EEG) signals. 
  • 1.2K
  • 13 Jul 2021
Topic Review
Hibernation
Torpor and hibernation are natural physiological processes. Torpor refers to a pe-riod of metabolic suppression with a duration from a few hours to several weeks. The state of torpor is probably older in evolutionary terms and was likely a survival strate-gy of protomammals. Hibernation is a more elaborate behavior, structured in many long bouts of torpor separated by brief interbouts of arousal.
  • 1.1K
  • 23 Feb 2021
Topic Review
TPC1 in plants
TPC1 in plants is localized in the vacuolar membrane. Its activity is strictly regulated by several factors emphasizing its complex structure and function. The physiological role of TPC1 is under debate. The TPC1 hyperactive version fou2 (carring D454N mutation) is characterized by an overproduction of jasmonate acid (JA), however the tpc1-2 knockout mutant has no pronounced phenotype. The intriguing concept of Ca2+-induced Ca2+ release was assigned to Vicia faba TPC1 in 1994 by Ward and Schroeder, however it has still not been confirmed for the model plant Arabidopsis thaliana.
  • 1.1K
  • 27 Oct 2020
Topic Review
Quantum Biology
Recent evidence suggests that a broad range of complex and dynamic processes in living systems could exploit quantum effects to enhance and/or regulate biological functions. These non-trivial quantum effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems so as to achieve biological advantages that cannot be understood within the boundaries of classical physics. Quantum biology is the study of such quantum aspects of living systems. 
  • 1.1K
  • 24 Mar 2021
Topic Review
Peptide Inhibitors of Kv1.5
The human voltage gated potassium channel Kv1.5 that conducts the IKur current is a key determinant of the atrial action potential. This channel is an attractive target for the management of Atrial Fibrillation (AF). A wide range of peptide toxins from venomous animals are targeting ion channels, including mammalian channels. These peptides usually have a much larger interacting surface with the ion channel compared to small molecule inhibitors and thus, generally confer higher selectivity to the peptide blockers. To date, literature has known two peptides that inhibit IKur: Ts6 and Osu1. T
  • 1.1K
  • 30 Dec 2021
Topic Review
Cell Cycle and Its Regulation
A decisive characteristic of life is the reproductive capacity of cells, which it does through a collection of highly complex and ordered regulatory process commonly known as the cell cycle. The cell cycle combines DNA replication with chromosomal segregation in an oscillatory manner. In this way, the cell cycle coordinates the precise replication of the genome through specific events to ensure that the duplicated genetic material is distributed equally to each daughter cell. The repetition of this process leads to the exponential proliferation of cells. This process is classically described as interphase and mitosis (M) phase. Most of the cell cycle is in interphase, which encompasses Gap 1 (G1), synthesis (S), and Gap 2 (G2) phases. During the interphase, the cell grows, replicates genetic materials, and repairs DNA damage and replication errors. M phase, a relatively short period, consists of prophase, metaphase, anaphase, and telophase, which completes the equal distribution of genome and cytoplasmic components. Following interphase, most nondividing cells exit the cell cycle at G1 into G0 phase (quiescence). G0 was originally used to describe cells that are not in the cell cycle but with the potential for division. The rate of cell cycling varies with the developmental stage and cell type. In general, the cell cycle is most active during development, as cells in early embryos can proliferate and differentiate to form tissues and organs. The cell cycle involves numerous life processes, and it is closely related to the growth and proliferation of eukaryotic cells, development of organisms, regulation of DNA damage repair, and occurrence of diseases.
  • 1.0K
  • 25 Jun 2021
Topic Review
β-Amyloid Vaccination
β-amyloid (Aβ) is a peptide, 38 to 43 amino acids long, that derives from the proteolytic processing of amyloid precursor protein (APP) by the γ-secretase; Aβ40 and Aβ42 are the most studied Aβ peptide species.
  • 1.0K
  • 20 Apr 2021
Topic Review
Photosensitive Substances
Photodynamic therapy (PDT) is part of photochemotherapy and requires the presence of a photosensitive substance (drug, PS), oxygen, and a powerful light source in the area of absorption of the PS used.
  • 1.0K
  • 13 Apr 2021
Topic Review
SARS-CoV-2 Nucleocapsid Protein
SARS-CoV-2 nucleocapsid protein (NCoV2) plays a key role in various processes related to the viral replication cycle such as the RNA genome packaging, interaction with other viral proteins. It has thus been a target for new drug development.
  • 1.0K
  • 27 May 2021
Topic Review
G-quadruplexes and ligands: Biophysical methods
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized in structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and x-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In the last years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most used approaches to characterize the G4/ligand interactions, as well as the applications and type of information that can be obtained from the use of each technique.
  • 1.0K
  • 03 Dec 2021
Topic Review
Magnetic nanoparticles: coating and applications
Magnetic nanoparticles (MNPs) have great potential in material science, drug delivery, magnetic resonance imaging, and therapeutic applications. Indeed, a number of iron oxide nanoparticles have been withdrawn due to their poor clinical performance and/or toxicity issues. MNPs have successfully been converted into water-soluble, stable, bio-accessible systems using the proprietary various coating strategy. Herein, we summarize the data of applications and coating strategies of MNPs.
  • 986
  • 11 Jan 2022
Topic Review
Negative Reversibly Switchable Fluorescent Proteins
The advancement of super-resolution imaging (SRI) relies on fluorescent proteins with novel photochromic properties. Using light, the reversibly switchable fluorescent proteins (RSFPs) can be converted between bright and dark states for many photocycles and their emergence has inspired the invention of advanced SRI techniques. The general photoswitching mechanism involves the chromophore cis-trans isomerization and proton transfer for negative and positive RSFPs and hydration–dehydration for decoupled RSFPs. However, a detailed understanding of these processes on ultrafast timescales (femtosecond to millisecond) is lacking, which fundamentally hinders the further development of RSFPs. For a negative RSFP such as Dronpa, the light used to induce fluorescence can often switch the protein from the on to off state; whereas for a positive RSFP like Padron, the same light can turn more proteins on. In contrast, the decoupled RSFPs can use separate light with different wavelengths for fluorescence excitation and photoswitching.
  • 979
  • 23 Jun 2022
Topic Review
Solubility and Aggregation of Proteins
Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the protein surface promotes the protein’s solubility in the polar environment. The application of 3D GAuss function allows identification of accordant/discordant regions in proteis. The discordant ones usually represent the localisation of biological activity. 
  • 974
  • 11 Oct 2021
Topic Review
Complex Nonlinear Biophysical Brain Dynamics
The human brain is a complex network whose ensemble time evolution is directed by the cumulative interactions of its cellular components, such as neurons and glia cells. Coupled through chemical neurotransmission and receptor activation, these individuals interact with one another to varying degrees by triggering a variety of cellular activity from internal biological reconfigurations to external interactions with other network agents. Consequently, such local dynamic connections mediating the magnitude and direction of influence cells have on one another are highly nonlinear and facilitate, respectively, nonlinear and potentially chaotic multicellular higher-order collaborations. Thus, as a statistical physical system, the nonlinear culmination of local interactions produces complex global emergent network behaviors, enabling the highly dynamical, adaptive, and efficient response of a macroscopic brain network.
  • 974
  • 07 Jun 2022
Topic Review
Allosteric Drug Discovery
Understanding molecular mechanisms underlying the complexity of allosteric regulation in proteins has attracted considerable attention in drug discovery due to the benefits and versatility of allosteric modulators in providing desirable selectivity against protein targets while minimizing toxicity and other side effects. The proliferation of novel computational approaches for predicting ligand–protein interactions and binding using dynamic and network-centric perspectives has led to new insights into allosteric mechanisms and facilitated computer-based discovery of allosteric drugs. Although no absolute method of experimental and in silico allosteric drug/site discovery exists, current methods are still being improved. As such, the critical analysis and integration of established approaches into robust, reproducible, and customizable computational pipelines with experimental feedback could make allosteric drug discovery more efficient and reliable. In this article, we review computational approaches for allosteric drug discovery and discuss how these tools can be utilized to develop consensus workflows for in silico identification of allosteric sites and modulators with some applications to pathogen resistance and precision medicine. The emerging realization that allosteric modulators can exploit distinct regulatory mechanisms and can provide access to targeted modulation of protein activities could open opportunities for probing biological processes and in silico design of drug combinations with improved therapeutic indices and a broad range of activities.
  • 973
  • 26 Sep 2021
Topic Review
Replication-Coupled Chromatin Remodeling
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks.
  • 968
  • 09 Mar 2021
Topic Review
Eye Movement Events
Eye tracking is the process of tracking the movement of the eyes to know exactly where and for how long a person is looking. Classifying raw eye-tracker data into eye movement events reduces the complexity of eye movement analysis.
  • 962
  • 25 Nov 2022
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