Experimental and Computational Methods to Assess Central Nervous System Penetration of Small Molecules.

In CNS drug discovery, the estimation of brain exposure to lead compounds is critical for their optimization. Compounds need to cross the blood-brain barrier (BBB) to reach the pharmacological targets in the CNS. The BBB is a complex system involving passive and active mechanisms of transport and efflux transporters such as P-glycoproteins (P-gp) and breast cancer resistance protein (BCRP), which play an essential role in CNS penetration of small molecules. Several in vivo, in vitro, and in silico methods are available to estimate human brain penetration. Preclinical species are used as in vivo models to understand unbound brain exposure by deriving the Kp,uu parameter and the brain/plasma ratio of exposure corrected with the plasma and brain free fraction. The MDCK-mdr1 (Madin Darby canine kidney cells transfected with the MDR1 gene encoding for the human P-gp) assay is the commonly used in vitro assay to estimate compound permeability and human efflux. The in silico methods to predict brain exposure, such as CNS MPO, CNS BBB scores, and various machine learning models, help save costs and speed up compound discovery and optimization at all stages. These methods enable the screening of virtual compounds, building of a CNS penetrable compounds library, and optimization of lead molecules for CNS penetration. Therefore, it is crucial to understand the reliability and ability of these methods to predict CNS penetration. We review the in silico, in vitro, and in vivo data and their correlation with each other, as well as assess published experimental and computational approaches to predict the BBB penetrability of compounds.

Microsecond molecular dynamics studies of cholesterol-mediated myelin sheath degeneration in early Alzheimer's disease.

Cholesterol-mediated perturbations of membrane structural integrity are key early events in the molecular pathogenesis of Alzheimer's disease (AD). In AD, protein misfolding (proteopathy) and pro-inflammatory conditions (immunopathy) culminate in neuronal death, a process enabled by altered membrane biophysical properties which render neurons more susceptible to proteopathic and immunopathic cytotoxicities. Since cholesterol is a principal neuronal membrane lipid, normal cholesterol homeostasis is central to membrane health; also, since increased cholesterol composition is especially present in neuronal myelin sheath (i.e. brain "white matter"), recent studies have not surprisingly revealed that white matter atrophy precedes the conventional biomarkers of AD (amyloid plaques, tau tangles). Employing extensive microsecond all-atom molecular dynamics simulations, we investigated biophysical and mechanical properties of myelin sheath membrane as a function of cholesterol mole fraction (χCHL). Impaired χCHL modulates multiple bilayer properties, including surface area per lipid (APL), chain order, number and mass density profiles, area compressibility and bending moduli, bilayer thickness, lipid tilt angles, H-bonding interactions and tail interdigitation. The increased orientational ordering of both palmitoyl and oleoyl chains in model healthy myelin sheath (HMS) membranes illustrates the condensing effect of cholesterol. With an increase in χCHL, number density profiles of water tend to attain bulk water number density more quickly, indicating shrinkage in the interfacial region with increasing χCHL. The average tilt value is 11.5° for the C10-C13 angle in cholesterol and 64.2° for the P-N angle in POPC lipids in HMS. These calculations provide a molecular-level understanding of myelin sheath susceptibility to pathology as an early event in the pathogenesis of AD.

Understanding the effect of nanoconfinement on the structure of water hydrogen bond networks.

Using an integrated approach of network theory and atomistic molecular dynamics simulations, we performed a detailed topological analysis on hydrogen bond networks of water confined between either two graphene sheets or two lipid bilayers to explore the structural perturbation of these networks under nanoscale confinement. The hydrogen bond network structure can be perturbed to a considerable extent when water is confined by such surfaces, yet no small-world behaviour is observed. The presence of ions also reduces the network complexity but its effect may be small depending on the type of confining surfaces. We developed an information flow model to evaluate the fluctuating nature of hydrogen bond networks and to characterise the dynamic, long-distance hydrogen-bonded chains in water. We found that the length and directionality of the hydrogen bond "trails" are highly susceptible to the type of confining surfaces and the degree of confinement. In particular, the endpoints of the hydrogen bond trails are not completely random in confined water, in which inherent distributions are determined by the density of water and the density of hydrogen bonds. This work forms the basis for the study of the pure effect of hydrogen bond network topology on various transport processes, such as proton transfer, that occur along a sequence of hydrogen bonds in a biochemical system. Our results suggest that a combined effect of the structure and lifetime of the hydrogen bond network of interfacial water may contribute to high lateral proton diffusivity at the surface of a lipid membrane.

Inhibition of Pantothenate Synthetase by Analogs of ß-Alanine Precursor Ineffective as an Antibacterial Strategy.

BACKGROUND: Pantothenate, the fundamental precursor to coenzyme A, is required for optimal growth and virulence of microbial pathogens. It is synthesized by the enzyme-catalyzed condensation of ß-alanine and pantoate, which has shown susceptibility to inhibition by analogs of its molecular constituents. Accordingly, analogs of ß-alanine are gaining inquiry as potential antimicrobial chemotherapeutics. METHODS: We synthesized and evaluated 35 derivatives of ß-alanine, substituted at the α, ß, amine, and carboxyl sites, derived from in silico, dynamic molecular modeling to be potential competitive inhibitors of pantothenate synthetase. Employing the Clinical Laboratory Standards M7-A6 broth microdilution method, we tested these for inhibition of growth in Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. RESULTS: All compounds proved entirely ineffective in all species tested, with no inhibition of growth being observed up to 200 µM/mL. CONCLUSIONS: Upon revision of the literature, we conclude that high enzyme selectivity or external salvage mechanisms may render this strategy futile against most bacteria.

Descending Colon Metastasis of Renal Cell Carcinoma: An Unusual Site of Metastasis.

Renal cell carcinoma (RCC) has a high metastatic potential. While metastasis to common sites like the lungs, liver, bones, and brain is well-documented, metastasis to the colon, particularly the descending colon, remains an uncommon occurrence. When RCC does metastasize to the gastrointestinal tract, it commonly spreads to the small bowel and stomach. There are few cases reported in literature involving RCC metastasis to the colon. The commonly affected areas within the colon include the rectosigmoid colon, splenic flexure, and transverse colon. We describe an 87-year-old male with a history of stage III RCC diagnosed three years ago, followed by left-sided nephroureterectomy, partial adrenalectomy, and perinephric lymph node dissection. He presented to the emergency department (ED) with melena and generalized abdominal pain for one week. Stool occult blood was positive. Computed tomography (CT) of the abdomen was significant for stable postsurgical changes related to prior left nephrectomy and colonic mass at the proximal descending colon. A colonoscopy revealed a necrotic appearing friable mass in the descending colon. The pathology of the mass revealed proliferated atypical cells positive for paired box 8 (PAX8), a cluster of differentiation 10 (CD10), RCC, and pan-cytokeratin and negative for caudal-type homeobox 2 (CDX2), thyroid transcription factor-1 (TTF-1), and a cluster of differentiation 68 (CD68), consistent with metastatic RCC.

Alzheimer's: The ABCDE Paradigm.

Alzheimer's disease (AD) and related dementias constitute a worldwide health crisis for which the design and development of global solutions is a neuropharmacologic priority. The much-publicized failures of multiple investigational agents for AD over the past 20 years drive the need to rethink our approach to therapeutics development. Herein we present the ABCDE paradigm as a conceptual tool to facilitate the development of safe, effective therapies for AD cure: (A) accessible; (B) blood-brain barrier permeant; (C) cognitive enhancing; (D) disease-modifying; (E) environmentally nontoxic.

Axonal plasma membrane-mediated toxicity of cholesterol in Alzheimer's disease: A microsecond molecular dynamics study.

Alzheimer's disease is increasingly being recognized as an immune-mediated disease of brain. Since physiological brain health and brain immune function is dependent upon homeostatic neuronal membrane structure and function, alterations in membrane lipid biochemistry may predispose to disease. Brain is rich in cholesterol, and cholesterol metabolism dysfunction is a known risk factor for AD. Employing extensive microsecond all-atom molecular dynamics simulations, we investigated the properties of model neuronal membranes as a function of cholesterol concentration; phospholipid and phospholipid/cholesterol bilayers were also simulated to compare against available experimental data. Increased cholesterol concentrations compact and stiffen the lipid membrane, reducing permeability while modulating local water densities in the peri-membranous environment. Conversely, lower cholesterol mole fraction yields membranes with increased molecular disorder, enhanced fluidity, higher molecular tilting, and augmented interdigitation between bilayer leaflet lipids. Our findings provide a molecular insight on effect of cholesterol composition on various biochemical processes occurring at neuronal axon plasma membrane. These calculations also endeavor to establish a membrane-based link between cholesterol as an AD risk factor and possible AD pathology.

Modeling Differential Enthalpy of Absorption of CO2 with Piperazine as a Function of Temperature.

Temperature-dependent correlations for equilibrium constants (ln K) and heat of absorption (ΔHabs) of different reactions (i.e., deprotonation, double deprotonation, carbamate formation, protonated carbamate formation, dicarbamate formation) involved in the piperazine (PZ)/CO2/H2O system have been calculated using computational chemistry based ln K values input to the Gibbs-Helmholtz equation. This work also presents an extensive study of gaseous phase free energy and enthalpy for different reactions using composite (G3MP2B3, G3MP2, CBS-QB3, and G4MP2) and density functional theory [B3LYP/6-311++G(d,p)] methods. The explicit solvation shell (ESS) model and SM8T solvation free energy coupled with gaseous phase density functional theory calculations give temperature-dependent reaction equilibrium constants for different reactions. Calculated individual and overall reaction equilibrium constants and enthalpies of different reactions involved in CO2 absorption in piperazine solution are compared against experimental data, where available, in the temperature range 273.15-373 K. Postcombustion CO2 capture (PCC) is a temperature swing absorption-desorption process. The enthalpy of the solution directly correlates with the steam requirement of the amine regeneration step. Temperature-dependent correlations for ln K and ΔHabs calculated using computational chemistry tools can help evaluate potential PCC solvents' thermodynamics and cost-efficiency. These correlations can also be employed in thermodynamic models (e.g., e-UNIQUAC, e-NRTL) to better understand postcombustion CO2 capture solvent chemistry.

Protracted course of chemical meningitis following posterior fossa epidermoid cyst excision - A case report.

Background: Chemical meningitis, a subtype of aseptic meningitis, as a complication of posterior fossa surgery is not a rare complication. However, the description of a severe protracted course following the surgical resection of an epidermoid cyst has not been described in the current literature. Chemical meningitis is thought to be associated with a hyperreactive inflammatory response, mediated in part by interleukin (IL)-10, IL-1ß, and tumor necrosis factor-α, to the postoperative keratin debris from the spontaneous leakage or surgical release of epidermoid contents into subarachnoid spaces, which ultimately can result in patient symptoms of meningitis and hydrocephalus. Often, this remains mild and the recommended management includes a short course administration of corticosteroids. Case Description: The authors report such a case in a patient who underwent a redoresection for a fourth ventricular epidermoid cyst. Postoperatively, the patient returned several times with symptoms of meningitis and hydrocephalus requiring multiple hospitalizations in the ensuing months. The patient required emergent cerebrospinal fluid diversion, further posterior fossa exploration and an extended high-dose corticosteroid treatment regimen. Conclusion: The authors summarize the current understanding of the biochemical processes involved for the rare presentation of postoperative chemical meningitis.

COVID-19 as a Trigger of Brain Autoimmunity.

Entry of SARS-CoV-2 into the central nervous system (CNS) activates microglia, triggering chronic neuroinflammation and possibly neurodegeneration. The complex transcriptome of SARS-CoV-2 shares molecular similarities with diverse human CNS protein epitopes, leading to a cytokine storm and various autoantibodies, potentially culminating in an autoimmune state. A COVID-19 initiated CNS autoimmune cascade may occur via multiple pathways including molecular mimicry, bystander activation, epitope spreading, production of autoantibodies, and immortalization of effector B-cells.

A Series of 2-((1-Phenyl-1H-imidazol-5-yl)methyl)-1H-indoles as Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.

Indoleamine 2,3-dioxygenase 1 (IDO1) is a promising therapeutic target in cancer immunotherapy and neurological disease. Thus, searching for highly active inhibitors for use in human cancers is now a focus of widespread research and development efforts. In this study, we report the structure-based design of 2-(5-imidazolyl)indole derivatives, a series of novel IDO1 inhibitors which have been designed and synthesized based on our previous study using N1-substituted 5-indoleimidazoles. Among these, we have identified one with a strong IDO1 inhibitory activity (IC50 =0.16 µM, EC50 =0.3 µM). Structural-activity relationship (SAR) and computational docking simulations suggest that a hydroxyl group favorably interacts with a proximal Ser167 residue in Pocket A, improving IDO1 inhibitory potency. The brain penetrance of potent compounds was estimated by calculation of the Blood Brain Barrier (BBB) Score and Brain Exposure Efficiency (BEE) Score. Many compounds had favorable scores and the two most promising compounds were advanced to a pharmacokinetic study which demonstrated that both compounds were brain penetrant. We have thus discovered a flexible scaffold for brain penetrant IDO1 inhibitors, exemplified by several potent, brain penetrant, agents. With this promising scaffold, we provide herein a basis for further development of brain penetrant IDO1 inhibitors.

Encoding scheme for data storage and retrieval on DNA computers.

There has been exponential growth in the amount of data being generated on a daily basis. Such a huge amount of data creates a need for efficient data storage techniques. Due to the limitations of existing storage media, new storage solutions have always been of interest. There have been recent developments in order to efficiently use synthetic deoxyribonucleic acid (DNA) for information storage. DNA storage has attracted researchers because of its extremely high data storage density, about 1 exabyte/mm3 and long life under easily achievable conditions. This work presents an encoding scheme for DNA-based data storage system with controllable redundancy and reliability, the authors have also talked about the feasibility of the proposed method. The authors have also analysed the proposed algorithm for time and space complexity. The proposed encoding scheme tries to minimise the bases per letter ratio while controlling the redundancy. They have experimented with three different types of data with a value of redundancy as 0.75. In the randomised simulation setup, it was observed that the proposed algorithm was able to correctly retrieve the stored data in our experiments about 94% of the time. In the situation, where redundancy was increased to 1, the authors were able to retrieve all the information correctly in the proposed experiments.

The Brain Exposure Efficiency (BEE) Score.

The blood-brain barrier (BBB), composed of microvascular tight junctions and glial cell sheathing, selectively controls drug permeation into the central nervous system (CNS) by either passive diffusion or active transport. Computational techniques capable of predicting molecular brain penetration are important to neurological drug design. A novel prediction algorithm, termed the Brain Exposure Efficiency Score (BEE), is presented. BEE addresses the need to incorporate the role of trans-BBB influx and efflux active transporters by considering key brain penetrance parameters, namely, steady state unbound brain to plasma ratio of drug (Kp,uu) and dose normalized unbound concentration of drug in brain (Cu,b). BEE was devised using quantitative structure-activity relationships (QSARs) and molecular modeling studies on known transporter proteins and their ligands. The developed algorithms are provided as a user-friendly open source calculator to assist in optimizing a brain penetrance strategy during the early phases of small molecule molecular therapeutic design.

Small molecule therapeutics for COVID-19: repurposing of inhaled furosemide.

The novel coronavirus SARS-CoV-2 has become a global health concern. The morbidity and mortality of the potentially lethal infection caused by this virus arise from the initial viral infection and the subsequent host inflammatory response. The latter may lead to excessive release of pro-inflammatory cytokines, IL-6 and IL-8, as well as TNF-α ultimately culminating in hypercytokinemia ("cytokine storm"). To address this immuno-inflammatory pathogenesis, multiple clinical trials have been proposed to evaluate anti-inflammatory biologic therapies targeting specific cytokines. However, despite the obvious clinical utility of such biologics, their specific applicability to COVID-19 has multiple drawbacks, including they target only one of the multiple cytokines involved in COVID-19's immunopathy. Therefore, we set out to identify a small molecule with broad-spectrum anti-inflammatory mechanism of action targeting multiple cytokines of innate immunity. In this study, a library of small molecules endogenous to the human body was assembled, subjected to in silico molecular docking simulations and a focused in vitro screen to identify anti-pro-inflammatory activity via interleukin inhibition. This has enabled us to identify the loop diuretic furosemide as a candidate molecule. To pre-clinically evaluate furosemide as a putative COVID-19 therapeutic, we studied its anti-inflammatory activity on RAW264.7, THP-1 and SIM-A9 cell lines stimulated by lipopolysaccharide (LPS). Upon treatment with furosemide, LPS-induced production of pro-inflammatory cytokines was reduced, indicating that furosemide suppresses the M1 polarization, including IL-6 and TNF-α release. In addition, we found that furosemide promotes the production of anti-inflammatory cytokine products (IL-1RA, arginase), indicating M2 polarization. Accordingly, we conclude that furosemide is a reasonably potent inhibitor of IL-6 and TNF-α that is also safe, inexpensive and well-studied. Our pre-clinical data suggest that it may be a candidate for repurposing as an inhaled therapy against COVID-19.

Understanding Carbamate Formation Reaction Thermochemistry of Amino Acids as Solvents for Postcombustion CO2 Capture.

The carbamate stability constant for a data set of 10 amino acids, having potential for being postcombustion CO2 capture (PCC) solvents, has been calculated using various implicit and explicit solvation shell models. This work also includes an extensive study of gas-phase free energy and enthalpy for the amino acid carbamate formation reaction with the Hartree Fock method, density functional methods [B3LYP/6-311++G(d,p)], and composite methods (G3MP2B3, G3MP2, CBS-QB3, and G4MP2). Ideal PCC solvent properties require finding a profitable tradeoff between various thermodynamic and system optimization parameters. Benchmark gaseous-phase and solution-phase thermodynamic properties given in this work can help in making informed decisions when choosing promising PCC solvents. The temperature dependency of the carbamate stability constant of amino acids is predicted using PCM and SM8T implicit solvation models. PCC is a temperature swing absorption-desorption process, and the high-temperature sensitivity of the ln KcAmCOO- value is of vital importance in attaining cost-efficient processes.

Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface.

The anomalous properties of interfacial water at the surface of a lipid membrane and their implications on nearby chemical processes are well recognized. However, we have found that ion pairing thermodynamics may not be significantly affected by interfacial water in a classical, nonpolarizable force field. To trace the root cause of such a counterintuitive finding, we performed atomistic molecular dynamics simulations to explore the impact of polarizable interactions and characterize the hydration structure of a sodium chloride (NaCl) ion pair at the surface of a model lipid membrane and in a bulk phase. Our study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface. This study also forms the basis for the future design of a reaction coordinate that takes the behavior of the interfacial water into account.

The Blood-Brain Barrier (BBB) Score.

The blood-brain barrier (BBB) protects the brain from the toxic side effects of drugs and exogenous molecules. However, it is crucial that medications developed for neurological disorders cross into the brain in therapeutic concentrations. Understanding the BBB interaction with drug molecules based on physicochemical property space can guide effective and efficient drug design. An algorithm, designated "BBB Score", composed of stepwise and polynomial piecewise functions, is herein proposed for predicting BBB penetration based on five physicochemical descriptors: number of aromatic rings, heavy atoms, MWHBN (a descriptor comprising molecular weight, hydrogen bond donor, and hydrogen bond acceptors), topological polar surface area, and pKa. On the basis of statistical analyses of our results, the BBB Score outperformed (AUC = 0.86) currently employed MPO approaches (MPO, AUC = 0.61; MPO_V2, AUC = 0.67). Initial evaluation of physicochemical property space using the BBB Score is a valuable addition to currently available drug design algorithms.

Postcombustion CO2 Capture Solvent Characterization Employing the Explicit Solvation Shell Model and Continuum Solvation Models.

UNLABELLED: A study on the explicit and implicit solvation models for calculation of solvation free energy of ions and pKa of amino acids presented recently [ Gupta , M. ; J. Chem. THEORY: Comput. 2013 , 9 , 5021 - 5031 ] is extended for the study of amines and alkanolamines. Solvation free energies and pKa's of a data set of 25 amines and alkanolamines are calculated using the explicit solvation shell (ESS) model given by da Silva et al. [ J. Phys. Chem. A 2009 , 113 , 6404 ] and continuum solvation models (polarized continuum solvation model (PCM), SM8T, and DivCon). An extensive overview involving the gas-phase basicity and proton affinity, calculated using density functional methods (B3LYP/6-311++G(d,p)) and composite methods (G3MP2B3, G3MP2, CBS-QB3, G4MP2) and compared with corresponding experimental results for amines and alkanolamines, is also included in the present work. This data set was selected based on the components' potential as solvents for postcombustion CO2 capture (PCC) processes. Results of gaseous-phase thermochemistry and pKa obtained from different models employed in this work are analyzed against experimental results for obtaining error estimates involved in each theoretical model. The ESS model for the calculation of the solvation free energy of ions combined with composite methods for gaseous-phase thermochemistry is found to give reasonable accuracy for pKa calculations of amines and alkanolamines and thereby constitutes a method for validation of pKa for new potential PCC solvents.

A versatile valving toolkit for automating fluidic operations in paper microfluidic devices.

Failure to utilize valving and automation techniques has restricted the complexity of fluidic operations that can be performed in paper microfluidic devices. We developed a toolkit of paper microfluidic valves and methods for automatic valve actuation using movable paper strips and fluid-triggered expanding elements. To the best of our knowledge, this is the first functional demonstration of this valving strategy in paper microfluidics. After introduction of fluids on devices, valves can actuate automatically after a) a certain period of time, or b) the passage of a certain volume of fluid. Timing of valve actuation can be tuned with greater than 8.5% accuracy by changing lengths of timing wicks, and we present timed on-valves, off-valves, and diversion (channel-switching) valves. The actuators require ~30 µl fluid to actuate and the time required to switch from one state to another ranges from ~5 s for short to ~50 s for longer wicks. For volume-metered actuation, the size of a metering pad can be adjusted to tune actuation volume, and we present two methods - both methods can achieve greater than 9% accuracy. Finally, we demonstrate the use of these valves in a device that conducts a multi-step assay for the detection of the malaria protein PfHRP2. Although slightly more complex than devices that do not have moving parts, this valving and automation toolkit considerably expands the capabilities of paper microfluidic devices. Components of this toolkit can be used to conduct arbitrarily complex, multi-step fluidic operations on paper-based devices, as demonstrated in the malaria assay device.