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We present fluorogenic cationic organo chalcogens that are highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report the application of organoselenium and organosulfur-based cell-permeable red-emissive probes bearing a favorable cyclic sidearm for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interacting with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes., QC 20221109

The current global health emergency in the form of the Coronavirus 2019 (COVID-19) pandemic has highlighted the need for fast, accurate, and efficient drug discovery pipelines. Traditional drug discovery projects relying on in vitro high-throughput screening (HTS) involve large investments and sophisticated experimental set-ups, affordable only to big biopharmaceutical companies. In this scenario, application of efficient state-of-the-art computational methods and modern artificial intelligence (AI)-based algorithms for rapid screening of repurposable chemical space [approved drugs and natural products (NPs) with proven pharmacokinetic profiles] to identify the initial leads is a powerful option to save resources and time. Structure-based drug repurposing is a popular in silico repurposing approach. In this review, we discuss traditional and modern AI-based computational methods and tools applied at various stages for structure-based drug discovery (SBDD) pipelines. Additionally, we highlight the role of generative models in generating molecules with scaffolds from repurposable chemical space., QC 20220718

A typical drug discovery project involves identifying active compounds with significant binding potential for selected disease-specific targets. Experimental high-throughput screening (HTS) is a traditional approach to drug discovery, but is expensive and time-consuming when dealing with huge chemical libraries with billions of compounds. The search space can be narrowed down with the use of reliable computational screening approaches. In this review, we focus on various machine-learning (ML) and deep-learning (DL)-based scoring functions developed for solving classification and ranking problems in drug discovery. We highlight studies in which ML and DL models were successfully deployed to identify lead compounds for which the experimental validations are available from bioassay studies., QC 20220718

GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries (FFTW, Intel MKL FFT, and FFT PACK). We break down the cost of each GROMACS computational phase and identify non-scalable stages, such as MPI communication during the 3D FFT computation when using a large number of processes. We show that the Particle-Mesh Ewald phase and the 3D FFT calculation significantly impact the GROMACS performance. Finally, we discuss performance opportunities with a particular interest in developing GROMACS for the FFT calculations.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response. This journal is, QC 20220309

Manual welding and hemming processes don’t deliver higher speeds and efficiency resulting in reduced production rate. Hence, robotic hemming and welding processes are to be implemented to overcome the risk involved in manual welding and achieving greater efficiency. Based on the present system layout in a local automotive industry, a virtual work cell was created with various robot models, fixtures and work tools like clamps, welding guns, rollers, etc. The robot operations were simulated and checked for collision, zoning and the cycle time which was estimated for both the virtual and real work environment. The simulated work cell was replicated in the real environment and checked for any discrepancies with the virtual work cell. The estimated total process time of various processes carried out in the closure panel assembly line by both the automated method and conventional method was compared and the percentage reduction in the total process time was determined.

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response.

Tauopathies are a subclass of neurodegenerative diseases characterized by an accumulation of microtubule binding tau fibrils in brain regions. Diseases such as Alzheimer's (AD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and corticobasal degeneration (CBD) belong to this subclass. Development of tracers which can visualize and discriminate between different tauopathies is of clinical importance in the diagnosis of various tauopathies. Currently, several tau tracers are available for in vivo imaging using a positron emission tomography (PET) technique. Among these tracers, PBB3 is reported to bind to various types of tau fibrils with comparable binding affinities. In contrast, tau tracer AV-1451 is reported to bind to specific types of tau fibrils (in particular to AD-associated and CTE) with higher binding affinity and only show nonspecific or weaker binding toward tau fibrils dominant with 3R isoforms (associated with PiD). The tau fibrils associated with different tauopathies can adopt different microstructures with different binding site microenvironments. By using detailed studies of the binding profiles of tau tracers for different types of tau fibrils, it may be possible to design tracers with high selectivity toward a specific tauopathy. The microstructures for the tau fibrils from patients with AD, PiD, and CTE have recently been demonstrated by cryogenic electron microscopy (cryo-EM) measurements allowing structure-based in silico simulations. In the present study, we have performed a multiscale computational study involving molecular docking, molecular dynamics, free energy calculations, and QM fragmentation calculations to understand the binding profiles of tau tracer AV-1451 and its potential use for diagnosis of AD, CTE, and PiD tauopathies. Our computational study reveals that different affinity binding sites exist for AV-1451 in the tau fibrils associated with different tauopathies. The binding affinity of this tracer toward differe

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response.

Tauopathies are a subclass of neurodegenerative diseases characterized by an accumulation of microtubule binding tau fibrils in brain regions. Diseases such as Alzheimer's (AD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and corticobasal degeneration (CBD) belong to this subclass. Development of tracers which can visualize and discriminate between different tauopathies is of clinical importance in the diagnosis of various tauopathies. Currently, several tau tracers are available for in vivo imaging using a positron emission tomography (PET) technique. Among these tracers, PBB3 is reported to bind to various types of tau fibrils with comparable binding affinities. In contrast, tau tracer AV-1451 is reported to bind to specific types of tau fibrils (in particular to AD-associated and CTE) with higher binding affinity and only show nonspecific or weaker binding toward tau fibrils dominant with 3R isoforms (associated with PiD). The tau fibrils associated with different tauopathies can adopt different microstructures with different binding site microenvironments. By using detailed studies of the binding profiles of tau tracers for different types of tau fibrils, it may be possible to design tracers with high selectivity toward a specific tauopathy. The microstructures for the tau fibrils from patients with AD, PiD, and CTE have recently been demonstrated by cryogenic electron microscopy (cryo-EM) measurements allowing structure-based in silico simulations. In the present study, we have performed a multiscale computational study involving molecular docking, molecular dynamics, free energy calculations, and QM fragmentation calculations to understand the binding profiles of tau tracer AV-1451 and its potential use for diagnosis of AD, CTE, and PiD tauopathies. Our computational study reveals that different affinity binding sites exist for AV-1451 in the tau fibrils associated with different tauopathies. The binding affinity of this tracer toward differe

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response.

Tauopathies are a subclass of neurodegenerative diseases characterized by an accumulation of microtubule binding tau fibrils in brain regions. Diseases such as Alzheimer's (AD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and corticobasal degeneration (CBD) belong to this subclass. Development of tracers which can visualize and discriminate between different tauopathies is of clinical importance in the diagnosis of various tauopathies. Currently, several tau tracers are available for in vivo imaging using a positron emission tomography (PET) technique. Among these tracers, PBB3 is reported to bind to various types of tau fibrils with comparable binding affinities. In contrast, tau tracer AV-1451 is reported to bind to specific types of tau fibrils (in particular to AD-associated and CTE) with higher binding affinity and only show nonspecific or weaker binding toward tau fibrils dominant with 3R isoforms (associated with PiD). The tau fibrils associated with different tauopathies can adopt different microstructures with different binding site microenvironments. By using detailed studies of the binding profiles of tau tracers for different types of tau fibrils, it may be possible to design tracers with high selectivity toward a specific tauopathy. The microstructures for the tau fibrils from patients with AD, PiD, and CTE have recently been demonstrated by cryogenic electron microscopy (cryo-EM) measurements allowing structure-based in silico simulations. In the present study, we have performed a multiscale computational study involving molecular docking, molecular dynamics, free energy calculations, and QM fragmentation calculations to understand the binding profiles of tau tracer AV-1451 and its potential use for diagnosis of AD, CTE, and PiD tauopathies. Our computational study reveals that different affinity binding sites exist for AV-1451 in the tau fibrils associated with different tauopathies. The binding affinity of this tracer toward differe

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response.

Tauopathies are a subclass of neurodegenerative diseases characterized by an accumulation of microtubule binding tau fibrils in brain regions. Diseases such as Alzheimer's (AD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and corticobasal degeneration (CBD) belong to this subclass. Development of tracers which can visualize and discriminate between different tauopathies is of clinical importance in the diagnosis of various tauopathies. Currently, several tau tracers are available for in vivo imaging using a positron emission tomography (PET) technique. Among these tracers, PBB3 is reported to bind to various types of tau fibrils with comparable binding affinities. In contrast, tau tracer AV-1451 is reported to bind to specific types of tau fibrils (in particular to AD-associated and CTE) with higher binding affinity and only show nonspecific or weaker binding toward tau fibrils dominant with 3R isoforms (associated with PiD). The tau fibrils associated with different tauopathies can adopt different microstructures with different binding site microenvironments. By using detailed studies of the binding profiles of tau tracers for different types of tau fibrils, it may be possible to design tracers with high selectivity toward a specific tauopathy. The microstructures for the tau fibrils from patients with AD, PiD, and CTE have recently been demonstrated by cryogenic electron microscopy (cryo-EM) measurements allowing structure-based in silico simulations. In the present study, we have performed a multiscale computational study involving molecular docking, molecular dynamics, free energy calculations, and QM fragmentation calculations to understand the binding profiles of tau tracer AV-1451 and its potential use for diagnosis of AD, CTE, and PiD tauopathies. Our computational study reveals that different affinity binding sites exist for AV-1451 in the tau fibrils associated with different tauopathies. The binding affinity of this tracer toward differe

We present here a new insight into the chemical reactivity and bioactivity of dopamine (DA) and gallic acid (GA) and their hyaluronic acid (HA) conjugates. Our data suggest that HA-GA scaffolds are superior to HA-DA, with higher oxidation kinetics, improved tissue adhesive properties, and radical scavenging ability with a lower pro-inflammatory response.

Tauopathies are a subclass of neurodegenerative diseases characterized by an accumulation of microtubule binding tau fibrils in brain regions. Diseases such as Alzheimer's (AD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and corticobasal degeneration (CBD) belong to this subclass. Development of tracers which can visualize and discriminate between different tauopathies is of clinical importance in the diagnosis of various tauopathies. Currently, several tau tracers are available for in vivo imaging using a positron emission tomography (PET) technique. Among these tracers, PBB3 is reported to bind to various types of tau fibrils with comparable binding affinities. In contrast, tau tracer AV-1451 is reported to bind to specific types of tau fibrils (in particular to AD-associated and CTE) with higher binding affinity and only show nonspecific or weaker binding toward tau fibrils dominant with 3R isoforms (associated with PiD). The tau fibrils associated with different tauopathies can adopt different microstructures with different binding site microenvironments. By using detailed studies of the binding profiles of tau tracers for different types of tau fibrils, it may be possible to design tracers with high selectivity toward a specific tauopathy. The microstructures for the tau fibrils from patients with AD, PiD, and CTE have recently been demonstrated by cryogenic electron microscopy (cryo-EM) measurements allowing structure-based in silico simulations. In the present study, we have performed a multiscale computational study involving molecular docking, molecular dynamics, free energy calculations, and QM fragmentation calculations to understand the binding profiles of tau tracer AV-1451 and its potential use for diagnosis of AD, CTE, and PiD tauopathies. Our computational study reveals that different affinity binding sites exist for AV-1451 in the tau fibrils associated with different tauopathies. The binding affinity of this tracer toward differe

Abnormal deposition of hyperphosphorylated tau as neurofibrillary tangles (NFTs) is an important pathological hallmark of Alzheimer's disease (AD) and of other neurodegenerative disorders. A noninvasive positron emission tomography (PET) tracer that quantifies neurofibrillary tangles in vivo can enhance the clinical diagnosis of AD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the tau fibril in the brain. In this paper, we study the binding profile of fibrillar tau aggregates with a PET tracer PI2620, which is a new second generation tau PET tracer that is presently experimentally and clinically studied. The target structure for the tau fibril is based on cryo-electron microscopy (cryo-EM) structure. A multiscale simulation workflow including molecular docking, molecular dynamics simulation, metadynamics simulation, and free energy calculations was implemented. We find that PI2620 can bind to eight surface binding sites, three core binding sites, and one entry site. The binding at the core sites and entry site is found to be much more favorable than that on the surface sites due to stronger hydrophobic interactions and less solvent exposure. Furthermore, the entry site which is formed by the terminal beta-sheets of the fibril is found to have the highest binding affinity to PI2620. Importantly, the binding capacity at the entry site can be much higher than that at other core sites, due to its easy accessibility. Therefore, the entry site is believed to be the major binding site for PI2620. A previous computational study on tracers with tau fibrils reports a maximum of four binding sites. Through use of methods that allow us to locate "cryptic binding sites", we report here additional core sites available for binding and we address the limitation of using the cryo-EM structure alone for structure-based tracer design. Our results could be helpful for elucidating the binding mechanism of imaging tracers with, QC 20200525

Purpose Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). Methods Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. Results The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme. Conclusions The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

Purpose Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). Methods Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. Results The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme. Conclusions The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

Purpose Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). Methods Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. Results The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme. Conclusions The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

Purpose Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). Methods Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. Results The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme. Conclusions The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

Purpose Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). Methods Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. Results The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme. Conclusions The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

Using the recently reported cryo-EM structure for the tau fibril [Fitzpatrick et al. (2017) Nature 547, 185-190], which is a potential target concerning Alzheimer's disease, we present the first molecular modeling studies on its interaction with various positron emission tomography (PET) tracers. Experimentally, based on the binding assay studies, at least three different high affinity binding sites have been reported for tracers in the tau fibril. Herein, through integrated modeling using molecular docking, molecular dynamics, and binding free energy calculations, we provide insight into the binding patterns of various tracers to the tau fibril. We suggest that there are four different high affinity binding sites available for many of the studied tracers showing varying binding affinity to different binding sites. Thus, PBB3 binds most strongly to site 4, and interestingly, this site is not a preferable site for any other tracers. For THIC5351, our data show that it strongly binds to sites 3 and 1, the former one being more preferable. We also find that MK6240 and T807 bind to site 1 specifically. The modeling data also give some insight into whether a tracer bound to a specific site can be replaced by others or not. For example, the displacement of T807 by PBB3 as reported experimentally can also be explained and attributed to the larger binding affinity of the latter compound in all binding sites. The binding free energy results explain very well the small binding affinity of THK523 compared to all the aryl quinoline moieties containing THK tracers. The ability of certain tau tracers, like FDDNP and THK523, to bind to amyloid fibrils has also been investigated. Furthermore, such off-target interaction of tau tracers with amyloid beta fibrils has been validated using a quantum mechanical fragmentation approach.

Understanding the mechanism of fibrilization of amyloid forming peptides could be useful for the development of therapeutics for Alzheimer disease (AD). Taking this standpoint, we have explored in this work the free energy profile for the inter-conversion of monomeric and dimeric forms of amyloid forming peptides into different secondary structures namely beta-sheet, helix and random coil in aqueous solution using umbrella sampling simulations and density functional theory calculations. We show that the helical structures of amyloid peptides can form beta sheet rich aggregates through random coil conformations in aqueous condition. Recent experiments (Chemistry. 2018, 24, 3397-3402 and ACS Appl. Mater. Interfaces, 2017, 9, 21116–21123) show that Molybdenum disulphide nanosurface and nanoparticles can reduce the fibrilization process of amyloid beta peptides. We have unravelled the free energy profile for the inter-conversion of helical forms of amyloid forming peptides into beta-sheet and random coil in the presence of a two dimensional nanosurface of (MoS2). Results indicate that the monomer and dimeric forms of the peptides adopt the random coil conformation in the presence of MoS2 while the helical form is preferable for the monomeric form and that the beta-sheet and helix forms are the preferable forms for dimers in aqueous solution. This is due to strong interaction with MoS2 and intra-molecular hydrogen bonds of random coil conformation. The stabilization of random coil conformation does not lead to beta sheet like secondary structure for aggregate. Thus the confinement of MoS2 promotes deaggregation of amyloid beta peptides rather than aggregation, something that could be useful for the development of therapeutics for AD.

Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However{,} the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al.{,} Proc. Natl. Acad. Sci. U. S. A.{,} 2017{,} 114(49){,} 13018–13023). Based on a multiscale modeling approach{,} here{,} we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers{,} we also show multiple binding sites in amyloid fibrils for this probe. In particular{,} BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4{,} a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites{,} it exhibited a less significant blue shift for the same absorption band.

The design of inhibitors for human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT) is one of the most successful approaches for the treatment of HIV infections. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) constitute a prominent drug class, which includes nevirapine, delavirdine, efavirenz, etravirine, and rilpivirine approved for clinical use. However, the efficiency of many of these drugs has been undermined by drug-resistant variants of HIV-1 RT, and it therefore becomes inevitable to design novel drugs to cope with resistance. Here, we discuss various drug design strategies, which include traditional medicinal chemistry, computational chemistry, and chemical biology approaches. In particular, computational modeling approaches, including machine learning, empirical descriptors-based, force-field, ab initio, and hybrid quantum mechanics/molecular mechanics-based methods are discussed in detail. We foresee that these methods will have a major impact on efforts to guide the design and discovery of the next generation of NNRTIs that combat RT multidrug resistance.

Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However{,} the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al.{,} Proc. Natl. Acad. Sci. U. S. A.{,} 2017{,} 114(49){,} 13018–13023). Based on a multiscale modeling approach{,} here{,} we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers{,} we also show multiple binding sites in amyloid fibrils for this probe. In particular{,} BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4{,} a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites{,} it exhibited a less significant blue shift for the same absorption band.

Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However{,} the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al.{,} Proc. Natl. Acad. Sci. U. S. A.{,} 2017{,} 114(49){,} 13018–13023). Based on a multiscale modeling approach{,} here{,} we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers{,} we also show multiple binding sites in amyloid fibrils for this probe. In particular{,} BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4{,} a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites{,} it exhibited a less significant blue shift for the same absorption band.

Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However{,} the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al.{,} Proc. Natl. Acad. Sci. U. S. A.{,} 2017{,} 114(49){,} 13018–13023). Based on a multiscale modeling approach{,} here{,} we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers{,} we also show multiple binding sites in amyloid fibrils for this probe. In particular{,} BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4{,} a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites{,} it exhibited a less significant blue shift for the same absorption band.

Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However{,} the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al.{,} Proc. Natl. Acad. Sci. U. S. A.{,} 2017{,} 114(49){,} 13018–13023). Based on a multiscale modeling approach{,} here{,} we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers{,} we also show multiple binding sites in amyloid fibrils for this probe. In particular{,} BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4{,} a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites{,} it exhibited a less significant blue shift for the same absorption band.

Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature., Funding Agencies|Institute of Advanced Materials (IAAM) [00554/2013-16]; Swedish Institute (SI) [00037/2014]; Linkoping Initiative in Life Science Technologies (LIST); Vinoba Bhave Research Institute [VBRI 2016/Res-01]; Linkoping University; Swedish Research Council [VR-2016-06014]

Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature., Funding Agencies|Institute of Advanced Materials (IAAM) [00554/2013-16]; Swedish Institute (SI) [00037/2014]; Linkoping Initiative in Life Science Technologies (LIST); Vinoba Bhave Research Institute [VBRI 2016/Res-01]; Linkoping University; Swedish Research Council [VR-2016-06014]

Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature., Funding Agencies|Institute of Advanced Materials (IAAM) [00554/2013-16]; Swedish Institute (SI) [00037/2014]; Linkoping Initiative in Life Science Technologies (LIST); Vinoba Bhave Research Institute [VBRI 2016/Res-01]; Linkoping University; Swedish Research Council [VR-2016-06014]

Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature., Funding Agencies|Institute of Advanced Materials (IAAM) [00554/2013-16]; Swedish Institute (SI) [00037/2014]; Linkoping Initiative in Life Science Technologies (LIST); Vinoba Bhave Research Institute [VBRI 2016/Res-01]; Linkoping University; Swedish Research Council [VR-2016-06014]

In this study, we have demonstrated the use of a graphene sheet as a fundamental building block to obtain a highly ordered graphene-enzyme electrode for electrochemical biosensing. Firstly, thin graphene sheets were deposited on 1.00 mm thick copper sheet at 850 oC, via chemical vapour deposition (CVD), using acetylene (C2H2) as carbon source in an argon (Ar) and nitrogen (N2) atmosphere. An anionic surfactant was used to introduce electrostatic charges and increase wettability and hydrophilicity on the basal plane of the otherwise hydrophobic graphene, thereby facilitating the assembly of biomolecules on the graphene surface. The bioelectrocatalytic activity of the system was investigated by the assembly of glucose oxidase (GOx) on the surface of the graphene sheet by intermolecular attractive forces. The electrochemical sensing activity of the graphene-based system was explored as a model for bioelectrocatalysis. The bioelectrode exhibited a linear response to glucose concentration from 0.2 to 9.8 mM, with sensitivity of 0.087 µA/µM/cm2 and a detection limit of 0.12 µM (S/N=3). This work sets the stage for the use of acetylene-sourced graphene sheets as fundamental building blocks in the fabrication of electrochemical biosensors and other biocatalytic devices., Funding agencies: Swedish Research Council, Sweden [VR-2011-6058357]; Research Directorate of the Vaal University of Technology, South Africa

Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature., Funding Agencies|Institute of Advanced Materials (IAAM) [00554/2013-16]; Swedish Institute (SI) [00037/2014]; Linkoping Initiative in Life Science Technologies (LIST); Vinoba Bhave Research Institute [VBRI 2016/Res-01]; Linkoping University; Swedish Research Council [VR-2016-06014]

The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50 degrees between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70-80 degrees with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition., QC 20170117

To cope with the rapid evolution of the tissue engineering field, it is now essential to incorporate the use of on-site responsive scaffolds. Therefore, it is of utmost importance to find new Intelligent biomaterials that can respond to the physicochemical changes in the microenvironment. In this present report, we have developed biocompatible stimuli responsive polyaniline-multiwalled carbon nanotube/poly(N-isopropylacrylamide), (PANI-MWCNT/PNIPAm) composite nanofiber networks and demonstrated the physiological temperature coordinated cell grafting phenomenon on its surface. The composite nanofibers were prepared by a two-step process initiated with an assisted in situ polymerization followed by electro-spinning. To obtain a smooth surface in individual nanofibers with the thinnest diameter, the component ratios and electrospinning conditions were optimized. The temperature-gated rearrangements of the molecular structure are characterized by FTIR spectroscopy with simultaneous macromolecular architecture changes reflected on the surface morphology, average diameter and pore size as determined by scanning electron microscopy. The stimuli responsiveness of the nanofibers has first been optimized with computational modeling of temperature sensitive components (coil-like and globular conformations) to tune the mechanism for temperature dependent interaction during in situ scaffolding with the cell membrane. The nanofiber networks show excellent biocompatibility, tested with fibroblasts and also show excellent sensitivity to inflammation to combat loco-regional acidosis that delay the wound healing process by an in vitro model that has been developed for testing the proposed responsiveness of the composite nanofiber networks. Cellular adhesion and detachment are regulated through physiological temperature and show normal proliferation of the grafted cells on the composite nanofibers. Thus, we report for the first time, the development of physiological temperature gated, Funding Agencies|IGEN; Swedish Research Council [VR-20116058357]; LIST

To cope with the rapid evolution of the tissue engineering field, it is now essential to incorporate the use of on-site responsive scaffolds. Therefore, it is of utmost importance to find new Intelligent biomaterials that can respond to the physicochemical changes in the microenvironment. In this present report, we have developed biocompatible stimuli responsive polyaniline-multiwalled carbon nanotube/poly(N-isopropylacrylamide), (PANI-MWCNT/PNIPAm) composite nanofiber networks and demonstrated the physiological temperature coordinated cell grafting phenomenon on its surface. The composite nanofibers were prepared by a two-step process initiated with an assisted in situ polymerization followed by electro-spinning. To obtain a smooth surface in individual nanofibers with the thinnest diameter, the component ratios and electrospinning conditions were optimized. The temperature-gated rearrangements of the molecular structure are characterized by FTIR spectroscopy with simultaneous macromolecular architecture changes reflected on the surface morphology, average diameter and pore size as determined by scanning electron microscopy. The stimuli responsiveness of the nanofibers has first been optimized with computational modeling of temperature sensitive components (coil-like and globular conformations) to tune the mechanism for temperature dependent interaction during in situ scaffolding with the cell membrane. The nanofiber networks show excellent biocompatibility, tested with fibroblasts and also show excellent sensitivity to inflammation to combat loco-regional acidosis that delay the wound healing process by an in vitro model that has been developed for testing the proposed responsiveness of the composite nanofiber networks. Cellular adhesion and detachment are regulated through physiological temperature and show normal proliferation of the grafted cells on the composite nanofibers. Thus, we report for the first time, the development of physiological temperature gated, Funding Agencies|IGEN; Swedish Research Council [VR-20116058357]; LIST

Motivated by the outstanding properties of bis(BF2) core complexes as fluorophore probes, we present a systematic computational study of their vibrationally resolved one- and two-photon absorption spectra in vacuum and in solution. Electronic and vibrational structure calculations were performed using the coupled cluster CC2 method and the Kohn-Sham formulation of density functional theory (DFT). A nonempirical estimation of the inhomogeneous broadening, accomplished using the polarizable embedding (PE) approaches combined with time-dependent DFT and CC2 methods, is used as a key ingredient of the computational protocol employed for simulations of the spectral features in solution. The inhomogeneous broadening is also determined based on the Marcus theory employing linear response and state-specific polarizable continuum model (PCM) methods. It is found that the polarizable embedding CC2 and the state-specific PCM are the most successful approaches for description of environmental broadening. For the 1(1)A(g) -> 1(1)B(u) transition, the non-Condon effects can be safely neglected and a fair agreement between the simulated and experimental band shapes is found. In contrast, the shape of the vibrationally resolved band corresponding to the two-photon allowed 1(1)A(g) -> 2(1)A(g) transition is largely dominated by non-Condon effects. A generalized few-level model was also employed to analyze the mechanism of the electronic two-photon 1(1)A(g) -> 2(1)A(g) excitation. It was found that the most important optical channel involves the 1(1)B(u) excited state. Ramifications of the findings for general band shape modeling are briefly discussed., QC 20160415

The design of molecular probes and tracer molecules with specificity toward amyloid beta (A beta) fibrils is of paramount importance for the selective diagnosis of Alzheimer's disease. This requires a detailed understanding of the binding sites in amyloid targets, their number, and their binding mechanism for various tracer molecules. We adopt an integrated approach including molecular docking, molecular dynamics, and generalized Born-based free energy calculations to investigate site-specific interactions of different amyloid binding molecules. Our study reproduces the experimental results on the relative binding affinity of the tracers and amyloid binders and explains the feature of "multiple binding sites" in amyloid targets as probed by competition binding experiments. A major outcome of this study is that it is the core sites of the Afi fibrils that are responsible for the experimentally reported binding profiles of tracers in amyloid targets rather than the surface sites that received much focus in earlier investigations., QC 20161012

We study the linear and nonlinear optical properties of a well-known acid base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral double right arrow anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral double right arrow anionic and open neutral double right arrow dianionic, can contribute to the pH- dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe., QC 20161019

The design of molecular probes and tracer molecules with specificity toward amyloid beta (A beta) fibrils is of paramount importance for the selective diagnosis of Alzheimer's disease. This requires a detailed understanding of the binding sites in amyloid targets, their number, and their binding mechanism for various tracer molecules. We adopt an integrated approach including molecular docking, molecular dynamics, and generalized Born-based free energy calculations to investigate site-specific interactions of different amyloid binding molecules. Our study reproduces the experimental results on the relative binding affinity of the tracers and amyloid binders and explains the feature of "multiple binding sites" in amyloid targets as probed by competition binding experiments. A major outcome of this study is that it is the core sites of the Afi fibrils that are responsible for the experimentally reported binding profiles of tracers in amyloid targets rather than the surface sites that received much focus in earlier investigations.

In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the larg