Seeking mTORC1 Inhibitors Through Molecular Dynamics Simulation of Arginine Analogs Inhibiting CASTOR1.

BACKGROUND: Hyperactivity of the mechanistic target of rapamycin complex 1 (mTORC1) is implicated in a variety of diseases such as cancer and diabetes. Treatment may benefit from effective mTORC1 inhibition, which can be achieved by preventing arginine from disrupting the cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1)-GTPase-activating proteins toward RAGS subcomplex 2 (GATOR2) complex through binding with CASTOR1. An attractive idea is to determine analogues of arginine that are as competent as arginine in binding with CASTOR1, but without disrupting the CASTOR1-GATOR2 interaction. MATERIALS AND METHODS: Molecular dynamics simulations were performed for binding of arginine analogues with CASTOR1 and binding free energy, hydrogen bond formation, and root mean squared deviation and root mean square fluctuation kinetics were then calculated. RESULTS: The binding free energy calculations revealed that Nα-acetyl-arginine, citrulline, and norarginine have sufficient binding affinity with CASTOR1 to compete with arginine. The hydrogen bond analysis revealed that norarginine, Nα-acetyl-arginine and D-arginine have proficient H-bonds that can facilitate their entering the narrow binding pocket. CONCLUSION: Norarginine and Nα-acetyl-arginine are the top drug candidates for mTORC1 inhibition, with Nα-acetyl-arginine being the best choice.

Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders.

Early-life infections and associated neuroinflammation is incriminated in the pathogenesis of various mood disorders. Infection with human roseoloviruses, HHV-6A and HHV-6B, allows viral latency in the central nervous system and other tissues, which can later be activated causing cognitive and behavioral disturbances. Hence, this study was designed to evaluate possible association of HHV-6A and HHV-6B activation with three different groups of psychiatric patients. DNA qPCR, immunofluorescence and FISH studies were carried out in post-mortem posterior cerebellum from 50 cases each of bipolar disorder (BPD), schizophrenia, 15 major depressive disorder (MDD) and 50 appropriate control samples obtained from two well-known brain collections (Stanley Medical Research Institute). HHV-6A and HHV-6B late proteins (indicating active infection) and viral DNA were detected more frequently (p < 0.001 for each virus) in human cerebellum in MDD and BPD relative to controls. These roseolovirus proteins and DNA were found less frequently in schizophrenia cases. Active HHV-6A and HHV-6B infection in cerebellar Purkinje cells were detected frequently in BPD and MDD cases. Furthermore, we found a significant association of HHV-6A infection with reduced Purkinje cell size, suggesting virus-mediated abnormal Purkinje cell function in these disorders. Finally, gene expression analysis of cerebellar tissue revealed changes in pathways reflecting an inflammatory response possibly to HHV-6A infection. Our results provide molecular evidence to support a role for active HHV-6A and HHV-6B infection in BPD and MDD.

Altered Micro-RNA Degradation Promotes Tumor Heterogeneity: A Result from Boolean Network Modeling.

Cancer heterogeneity may reflect differential dynamical outcomes of the regulatory network encompassing biomolecules at both transcriptional and post-transcriptional levels. In other words, differential gene-expression profiles may correspond to different stable steady states of a mathematical model for simulation of biomolecular networks. To test this hypothesis, we simplified a regulatory network that is important for soft-tissue sarcoma metastasis and heterogeneity, comprising of transcription factors, micro-RNAs, and signaling components of the NOTCH pathway. We then used a Boolean network model to simulate the dynamics of this network, and particularly investigated the consequences of differential miRNA degradation modes. We found that efficient miRNA degradation is crucial for sustaining a homogenous and healthy phenotype, while defective miRNA degradation may lead to multiple stable steady states and ultimately to carcinogenesis and heterogeneity.

Chromosomally integrated human herpesvirus 6 in heart failure: prevalence and treatment.

AIMS: Human herpesvirus 6 (HHV-6) A and B are two betaherpesviruses that are associated with many conditions including roseola, drug-induced hypersensitivity syndrome, limbic encephalitis, and myocarditis. HHV-6 is integrated in the germline [chromosomically integrated HHV-6 (ciHHV-6)] in ∼0.8% of the human population. To date, the prevalence, species distribution, and treatment responses of ciHHV-6 are unknown for cardiac patients. METHODS AND RESULTS: We determined the prevalence of HHV-6 and ciHHV-6 genotypes in 1656 endomyocardial biopsies of patients with persisting unexplained symptoms of heart failure. Infection of cardiac tissue was identified by nested PCR, electron microscopy, and immunohistochemistry. Virus load and mRNA levels were followed in ciHHV-6 patients treated with ganciclovir. HHV-6 was detected in 273 of 1656 cardiac tissues (16.5%; HHV-6B, 98.2%, HHV-6A, 1.8%) by PCR. Nineteen of the 1656 patients (1.1%) presented with persistently high HHV-6 copy numbers indicative of ciHHV-6. Sequencing confirmed ciHHV-6A in seven patients (36.8%) which was considerably higher than detected in non-ciHHV-6 patients. Inheritance was demonstrated in three selected families, confirming ciHHV-6 chromosomal integration by PCR and fluorescence in situ hybridization. HHV-6 reactivation and chromosomal integration were confirmed in peripheral blood mononuclear cells and heart tissue. Virus particles were identified in degenerating myocytes and interstitial cells. Antiviral treatment abolished viral mRNA and ameliorated cardiac symptoms. CONCLUSION: Virus replication in cardiac tissue of ciHHV-6 heart failure patients suggests that ciHHV-6 reactivation causes persistence of unexplained heart failure symptoms. We demonstrated that antiviral treatment, effective in decreasing viral transcripts and clinical complaints of cardiomyopathies, is a new therapeutic option for ciHHV-6-associated diseases.

Computational analysis of mTOR signaling pathway: bifurcation, carcinogenesis, and drug discovery.

Molecularly targeted therapeutics provides potentially more reliable performance while significantly reducing toxicity in comparison with chemotherapy. For cancer signaling networks which are usually complex, multiple molecules should be simultaneously targeted in order to stay in tune with the control mechanisms of the network and to achieve the maximum synergistic effects. Mathematical modeling and computer simulation are important in reproducing the dynamics of the network, some of which may correspond to healthy or cancer phenotypes. More importantly, the effects of multiple molecules can be simulated by perturbing many parameters in the model. In this paper, through the example of the mTOR signaling pathway, we demonstrate that computational analysis can provide great insights into cancer pathogenesis and the possible therapeutic interventions. In particular, we discovered a composite parameter which summarizes the synergistic effects of four different parameters. The geometry of the parameter space could be helpful in the development of a low dosage, minimal toxicity drug to cure cancer.

The impact of declining clinical autopsy: need for revised healthcare policy.

In Western countries, autopsy rates for patients deceased in hospitals have dropped to record lows, while the average frequency of major errors in clinical diagnoses has more than doubled during the same time period. Meanwhile, the Institute of Medicine and the U.S. Department of Health and Human Services have called attention to the high frequency of errors affecting patient safety, bringing the issue of public safety to the forefront of public health concerns. Although autopsies represent a vital tool for the acquisition of new medical knowledge and for medical quality assurance, health care professionals, insurers, and politicians apparently have not chosen the right approach to solve the problem of declining autopsy rates. The present article reviews the current status of clinical autopsies and addresses causes and consequences of their neglect and appeal the urgent need to revise the policy for clinical autopsy.

Feed-forward and feedback mechanisms in a dynamic model of human T cell development and regulation.

We describe a computational model of human T cell regulatory dynamics. We used this model to simulate changes in T cell pool numbers and for studying feedback and feed-forward responses in and among these pools. The pools identified were the bone marrow stem cell compartment, early and late thymocyte compartments and the peripheral compartment of mature T lymphocytes. Simulated data showed variable intercompartmental strengths indicative of a range of sensitivities to feedback regulation and respective variable feed-forward responses. The results compare well to known clinical and experimental data, rendering the computational model a good basis for further research in T cell development and regulation.

A simple model to simulate cellular changes in the T cell system following HIV-1 infection.

A new mathematical model is presented to simulate various changes of cell pools in the T cell immune system with validation procedures imitating viral infections. The present paper focuses on changes during the course of an acute progressive HIV-1 infection. Parameters are optimized by a direct search method and the stability of the model is studied. Mathematical modeling supports the hypothesis that the differentiation blockade is one major reason for the depletion of CD4 cells and the proliferation of CD38 cells in HIV-1 infection. The model appears to be a useful basis for further simulating disturbances of the T cell immune system in other viral infections as well as to elucidate the pathogenesis of various immunological diseases including the development of malignant lymphomas.

A continuous model studying T cell differentiation and lymphomagenesis and its distinction with discrete models.

The development of T-lymphocytes (T cells) constitute one of the basic and most vital processes in immunology. Conventional mathematical models, being based on the systems theory, fail to sufficiently distinguish the constituents of thymocytes and are thus of limited significance. On the basis of some well thought-out definitions and concepts, a continuous model was designed to describe T cell maturation in the thymus. A partial differential equation was first derived through the analysis of an infinitesimal element of the flow of thymocytes. A computation scheme was designed to determine the growth field in the thymus based upon available experimental data. The corresponding algorithm proved quite simple. A numerical example is given that focuses on the DN stage of the T cell development. The model opens a window for investigating the thymic microenvironment. The potential of the model in studying lymphomagenesis is discussed.

A general mathematical method for investigating the thymic microenvironment, thymocyte development, and immunopathogenesis.

T-lymphocyte (T-cell) development constitutes one of the basic and most vital processes in immunology. The process is profoundly affected by the thymic microenvironment, the dysregulation of which may be the pathogenesis or the etiology of some diseases. On the basis of a general conceptual framework, we have designed the first biophysical model to describe thymocyte development. The microclimate within the thymus, which is shaped by various cytokines, is first conceptualized into a growth field lambda and a differentiation field mu, under the influence of which the thymocytes mature. A partial differential equation is then derived through the analysis of an infinitesimal element of the flow of thymocytes. A general method is presented to estimate the two fields based on experimental data obtained by flow cytometric analysis of the thymus. Numerical examples are given for both normal and pathologic conditions. Our results are quite good, and even the time varying fields can be accurately estimated. Our method has demonstrated its great potential for the study of immunopathogenesis. The plan for implementation of the method is addressed.

Human herpesvirus-6: a short review of its biological behavior.

HHV-6 shows a widespread distribution with life-long persistence. The virus is frequently reactivated, yet remains clinically inapparent unless the patient is immunodeficient in some way. Even then, HHV-6 reactivation may simply enhance the pathogenicity of other viruses or existing autoimmune disorders rather than becoming a pathogen itself. Future clinical studies need to focus on such indirect viral influences mediated through molecular mimicry and interference with cell receptor expression, and cytokine and chemokine network regulation. Nevertheless, such disturbances may afford therapeutic intervention to disrupt herpesvirus interference and improve certain disease processes. There are only a few diseases for which an immediate causal relationship to HHV-6 infection has been suggested.

Mathematical model to simulate the cellular dynamics of infection with human herpesvirus-6 in EBV-negative infectious mononucleosis.

Acute infection with human herpesvirus-6 induces physiological cell proliferation in persons without major immune deficiency. It thus can serve as a parameter to validate a mathematical model designed to simulate cell proliferation under physiological and pathological conditions. Such a mathematical model is presented to simulate various cell changes of the T-cell immune system during the course of HHV-6 infection. Model development follows several steps, beginning with a basic model containing physiological T-cell pools to the introduction of infectious stimuli in the final model. A search algorithm designed to optimize the system parameters, as well as initial variables of the model, is presented. The results of simulation runs for acute HHV-6 infection of the final computational model correspond well to the data, as documented in human patients; they suggest that the computational model presented for the simulation of T-cell levels in a given viral infection may well serve as a tool for similar studies of other viral infections, including those that lead to cellular aplasia or neoplasia.

A simplified and comprehensive computational model to study the behavior of T cell populations in the thymus during normal maturation and in infection with mouse moloney leukemiavirus.

Based on a previously developed theory of dysregulative lymphoma pathogenesis, an advanced mathematical model was developed for simulation of thymic T cell populations and their differentiation stages. The model subsequently was tested in comparison to thymic changes in mice with Moloneyvirus infection and leukemia development. Numerical examples are given, which suggest that the model is useful to study T cell proliferation, differentiation, and may probably also be useful to simulate T cell changes in various lymphoproliferative diseases.

Growth factors, cytokines, chemokines and neuropeptides in the modeling of T cells. Part II: Data tables of normal values in man.

Members of the T lymphocyte lineage belong to a highly reactive cell system engaged in the control of internal homoeostasis and bodily intactness. It fulfills its commitments in close communication with the cellular and non-cellular microenvironment and with neuroendocrine regulatory mechanisms. The tools of such communication are various substances and compounds identified as cytokines, chemokines, hormones, growth factors, neuropeptides and components of the extracellular matrix. In a previous publication (22) we described the major players in the network regulation of T cell development and function as a basis for a computational modeling study. The present paper summarizes normal reference values for serum and/or plasma concentrations of these factors in man.

TCM-1: a nonlinear dynamical computational model to simulate cellular changes in the T cell system; conceptional design and validation.

Based upon a previously developed theory of dysregulative lymphoma pathogenesis, a computer model is designed in order to simulate cell changes occurring in disturbances of the T cell immune system and in lymphoproliferative diseases. The model is based upon the concept that factors identified as proliferation factors, differentiation factors and inhibition factors exert a network regulation upon development and function of the T cell system, and that selective disturbances of these factors may lead to hyperplastic, aplastic or neoplastic diseases. The resulting computer model (TCM-1) was validated by comparing it with data from human diseases such as acute HHV-6 (viral) infection, chronic persistent HHV-6 infection, progressive HIV1 infection and HTLV-1 infection, and comparing the simulation results with the actual cell data in the human patients. All these infections target the same T cell population (i.e. CD4 + T helper cells), yet cause different prototypical reactions (hyperplastic, aplastic, neoplastic). The described computer model, which was successfully used to simulate changes in the benign lymphoproliferative disease, Canale-Smith syndrome, will serve as the basis model for further supplementation to accommodate identified factorial influences such as by cytokines, chemokines and others.

Human herpesvirus-6 has no apparent influence on course of HCV hepatitis, but may complicate HBV hepatitis and alcoholic liver disease. A pilot study.

Human herpesvirus-6 (HHV-6) is a widespread virus with occasional reactivation and a potential hepatotropism. The present study was undertaken to investigate the frequency of HHV-6 reactivation in viral (HCV, HBV) and alcoholic liver diseases and its implication for the course of the primary disease. Serological and immunohistochemical tests were done to document viral activity, hepatocellular apoptosis or proliferation, and autoantibody formation. While the course of HCV remains apparently uninfluenced by HHV-6, HBV hepatitis and alcoholic liver disease show a higher incidence of autoantibody formation if HHV-6 is present. The data of this pilot study warrant more extensive investigations of the clinical pathology of HHV-6 in liver diseases.

Growth factors, cytokines, chemokines and neuropeptides in the modeling of T-cells.

The T lymphocyte lineage, from initial stem cells to peripheral mature T-cells, are members of a highly reactive cell system engaged in the control of internal homoeostasis and body intactness. It fulfills its commitments in close communication with the cellular and non-cellular microenvironment and with neuroendocrine regulatory mechanisms. Tools of such communication are various substances and compounds identified as cytokines, chemokines, hormones, growth factors and neuropeptides. Any pathogenetical model of functional aberration and disease development in the T-cell system must take into account the delicate network control exerted by the above mechanisms. In the following we describe the major players in the network regulation of T-cell development and function as a basis for a computational modeling study.

A computational analysis of Canale-Smith syndrome: chronic lymphadenopathy simulating malignant lymphoma.

OBJECTIVE: The objective of this study was to simulate changes in the human T cell system representing Canale-Smith syndrome using a dynamic computer model of T cell development and comparing with available human data. STUDY DESIGN: Physiological stepwise maturation and function of T lymphocytes in the computer model is altered by introducing functional disturbances following lymphotropic virus infection. In the present model, acute and chronic persistent infection with the human herpesvirus-6 (HHV-6) was simulated, and ensuing changes in T cell populations were compared with those measured in human patients. RESULTS: Using our computer model we previously found that simulated acute HHV-6 infection produced T cell computer data, which resembled an infectious mononucleosis-like disease in patients. Simulated chronic persistent infection, instead, resulted in variable cell changes comparing well to patients with chronic fatigue syndrome. In one setting, however, persistent immature lymphocytosis was observed similar to what initial has been described in this journal as Canale-Smith syndrome. CONCLUSION: Using a computer model developed by us we were able to produce simulations that resemble the immune system features of Canale-Smith syndrome. Further understanding of these simulation results may possibly guide future investigations into this disorder.

Dynamics of HTLV-1 leukemogenesis: data acquisition for computer modeling.

A literature search for HTLV-1-induced adult T-cell leukemia (ATL) at the National Library of Medicine resulted in 1003 publications which were evaluated with regard to HTLV-1 virus load, apoptosis and peripheral blood leukocyte changes during the latent period and leukemia development following virus infection. The data are presented in a comparable way to previous publications of infections with HHV-6 and HIV (which target the same CD4+ cell for infection) to be used for computer validation studies. After initial infection, HTLV-1 remains clinically latent for many years at low provirus copy numbers in CD4 cells. Once immune surveillance deteriorates and viral replication progresses, provirus copy numbers increase rapidly. Unlike other virus infections, apoptotic death of virus-infected "atypical" lymphocytes decreases with increasing viral load, thus favoring continued proliferation of these cells and further virus replication at the same time. Changes in the peripheral blood are characterized by coincident rises in oligoclonal lymphocyte populations including HTLV-1-positive CD4+ T-lymphocytes and their precursors with a progressive shift to immature cells as disease progresses. The pathogenesis of HTLV-1-induced adult T-cell leukemia is an example of dysregulative leukemogenesis ideal for validation of respective computer simulation models.

Los virus herpes linfotrópicos humanos: epstein-Barr (VEB), 6 y 7 (HHV-6 y HHV-7) en la patogenia de enfermedades mielodisplásicas (SMD) y mieloproliferativas (SMP) / Lymphotropic human herpesviruses: epstein-Barr (EBV), 6 y 7 (HHV-6 and HHV-7) in the pathogenia of myelodysplastic (MDS) and mieloproliferative diseases (MPS)

Con base en alteraciones mielodisplásicas y mieloproliferativas observadas en pacientes con enfermedades linfoproliferativas asociadas a virus herpes linfotrópicos humanos, se realizaron estudios de escrutinio para demostrar eventualmente la reactivación de éstos y su posible implicación en la patogenia y curso de síndrome mielodisplásico (SMD) y de síndrome mieloproliferativo (SMP). Se investigaron 74 biopsias de médula ósea y sueros de pacientes con SMD y 49 biopsias de médula ósea y 36 sueros de pacientes con leucemia mieloide crónica (LMC), a 13 casos de México no se les realizó serología. El diagnóstico y clasificación se hizo según los criterios del Grupo Franco-Americano-Británico (FAB). Se realizaron pruebas séricas de anticuerpos contra antígeno de la cápsula viral (VCA) y antígeno temprano (EA) del VEB con las técnicas de ELISA y de inmunofluorescencia y de HHV-6 y HHV-7 mediante inmunofluorescencia. La inmunohistología se realizó con la técnica de APAAP (fosfatasa alcalina-antifosfatasa alcalina) para expresión antigénica de los 3 virus y por anticuerpos monoclonales. Se determinó proliferación celular con APAAP y con anticuerpo monoclonal contra el antígeno nuclear de proliferación celular (PCNA). Se encontraron títulos de IgG anti-VEB-EA en 62 por ciento de los casos con SMD y en 33 por ciento con LMC, títulos de IgG HHV-6 elevados en 19 por ciento de los casos con SMD y en 9.3 por ciento de LMC y los de HHV-7 elevados en el 37.8 por ciento y 13.9 por ciento, respectivamente. Los títulos de IgM fueron negativos para los tres virus. La expresión de antígeno en la médula ósea fue positiva en el 76 por ciento de SMD a VEB-EA, 48.6 por ciento a HHV-6 p41 y 37.8 por ciento a HHV-7. Los casos de LMC expresaron VEB-EA en el 77 por ciento, HHV-6 en el 54.5 por ciento y HHV-7 en el 21.8 por ciento.