Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach

Background

The increased sequencing of pathogen genomes and the subsequent availability of genome-scale functional datasets are expected to guide the experimental work necessary for target-based drug discovery. However, a major bottleneck in this has been the difficulty of capturing and integrating relevant information in an easily accessible format for identifying and prioritizing potential targets. The open-access resource TDRtargets.org facilitates drug target prioritization for major tropical disease pathogens such as the mycobacteria Mycobacterium leprae and Mycobacterium tuberculosis; the kinetoplastid protozoans Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi; the apicomplexan protozoans Plasmodium falciparum, Plasmodium vivax, and Toxoplasma gondii; and the helminths Brugia malayi and Schistosoma mansoni.

Methodology/Principal Findings

Here we present strategies to prioritize pathogen proteins based on whether their properties meet criteria considered desirable in a drug target. These criteria are based upon both sequence-derived information (e.g., molecular mass) and functional data on expression, essentiality, phenotypes, metabolic pathways, assayability, and druggability. This approach also highlights the fact that data for many relevant criteria are lacking in less-studied pathogens (e.g., helminths), and we demonstrate how this can be partially overcome by mapping data from homologous genes in well-studied organisms. We also show how individual users can easily upload external datasets and integrate them with existing data in TDRtargets.org to generate highly customized ranked lists of potential targets.

Conclusions/Significance

Using the datasets and the tools available in TDRtargets.org, we have generated illustrative lists of potential drug targets in seven tropical disease pathogens. While these lists are broadly consistent with the research community''s current interest in certain specific proteins, and suggest novel target candidates that may merit further study, the lists can easily be modified in a user-specific manner, either by adjusting the weights for chosen criteria or by changing the criteria that are included.     

Psychological problems associated with diagnosis and treatment of lymphomas. II: Prospective study.

A prospective study of 120 patients newly diagnosed as having Hodgkin''s disease and non-Hodgkin''s lymphoma was conducted to determine the nature, extent, and timing of the psychiatric and social morbidity associated with the diagnosis and treatment. Patients were interviewed at diagnosis and two, six, and 12 months later by trained interviewers using standardised questionnaires. Psychiatric morbidity was greatest in the three months before treatment, but new episodes of anxiety and depression developed throughout the year of follow up. Altogether 39 patients suffered a depressive illness or anxiety state, or both, and a further 37 experienced borderline anxiety or depression, or both, during the 15 months of assessment. The most common adverse effects of treatment were hair loss, nausea, vomiting, sore mouth, and changes in perception of taste. Toxicity of treatment was associated with psychiatric morbidity. Conditioned responses to chemotherapy were experienced by 32 patients. Social morbidity was low, although difficulties in returning to work and to previous levels of leisure activity were noted. Although most patients were no longer receiving treatment and were free of disease at the one year follow up, 51 patients continued to complain of loss of energy, 24 of loss of libido, 38 of tiredness, 23 of irritability, 18 of poor concentration, and 23 of memory impairment. These results confirm our retrospective study and suggest that a high price is paid for long term survival by a substantial proportion of patients receiving treatment for Hodgkin''s disease and non-Hodgkin''s lymphoma.     

Provision of hearing aids: does specialist assessment cause delay?

OBJECTIVE--To identify the main delay in the provision of hearing aids for people with impaired hearing and identify possible problems and short-comings caused by a community based hearing aid dispensing service. DESIGN--Prospective cohort analysis based on data collected from patients on the duration of hearing impairment, from the referral letters in respect of the general practitioners'' findings on otoscopy, and from the ear, nose, and throat assessment in the clinic with respect to the outcome of specialist otoscopy and management of the hearing impairment. SETTING--General ear, nose, and throat outpatient clinic. PATIENTS--100 Consecutive patients aged 19-94 referred by general practitioners for the provision of hearing aids or for assessment and treatment of impaired hearing. RESULTS--Most patients with impaired hearing did not seek medical advice for at least a year. The time from referral by the general practitioner to the provision of a hearing aid was under two months. General practitioners consistently recognised normality on otoscopy but failed to recognise abnormality in eight of 45 cases. Seven patients required further investigation to exclude serious disease and nine had conditions amenable to surgery. CONCLUSIONS--The main cause of delay in treating impaired hearing is failure by patients to seek help promptly. Specialist assessment of patients with impaired hearing is preferable and does not necessarily cause delay in providing hearing aids. The provision of hearing aids should remain a hospital based service.     

Management of Adult Acute Myelogenous Leukaemia

Consecutive adult patients admitted to St. Bartholomew''s Hospital with acute myelogenous leukaemia have been treated with a remission induction drug schedule consisting of daunorubicin and cytosine arabinoside. Intermittent five-day courses were used in 72 patients, and a complete remission was obtained in 39 patients (54%). An alternative drug schedule in 22 patients resulted in fewer remissions but this may have been due to age differences in the two groups. Age and initial platelet count were found to be important factors in determining the success of remission induction therapy; the older patients and those with low platelet counts responded less well.A series of 23 patients who achieved remissions was divided into two groups; one received intermittent combination chemotherapy as the only form of maintenance, and the other was given weekly immunotherapy in addition to the chemotherapy. The immunotherapy consisted of irradiated allogeneic leukaemic cells and B.C.G. Eight of the 10 patients on chemotherapy alone have already relapsed compared with five out of 13 patients in the immunotherapy group. It is hoped that these promising initial results with this form of maintenance will be confirmed as more patients enter the maintenance trials.     

Growth and toxin formation by Clostridium botulinum at low pH values

Spores of Clostridium botulinum were found to initiate growth and to produce toxin in aqueous suspensions of soya protein at pH values as low as 4-2 and in skimmed milk at pH 4.4. Most of the experiments were done with mixed cultures of CI. botulinum types A and B in the presence of two strains of Bacillus subtilis. The role of the latter organism was concluded to be to lower the oxygen content and the E_h of the suspensions. Toxin was produced at pH 4-4 after 4 weeks of incubation at 30^oC when either hydrochloric or citric acids were used as the acidulant and after 12 and 14 weeks when, respectively, lactic and acetic acids were used. Thus, amongst other factors the nature of the acid and not solely the pH value is an important factor in controlling the growth of Cl. botulinum at low pH. Pure cultures of Cl botulinum type A grew at 30^oC under strictly anaerobic conditions and produced toxin at pH 4-3 in the presence of hydrochloric acid.     

Structure of retroviral RNAs produced by cell lines derived from spontaneous lymphomas of AKR mice.

The retrovirus expression of eight independent lymphoid cell lines derived from spontaneous thymomas of AKR mice was investigated. The RNase T1 fingerprints of viral 70S RNA produced by these cell lines were compared with genome structures of the non-leukemogenic Akv virus and with two types of cloned leukemogenic viruses derived from one of the thymoma cell lines. Viral RNAs from three cell lines, SL3, 4, and 7, were indistinguishable from one another. The fingerprint patterns indicated that these cell lines produce equal amounts of two prototype, leukomogenic SL viruses that were previously isolated from the SL3 cell line. Viral RNA produced by the SL1 and SL2 cell lines contained similar components, but at a different ratio. Two other cell lines (SL5 and SL11) produced viral RNAs that resemble those of AKR mink cell focus-forming viruses. One additional line, SL9, produced viral RNA of a novel structure. The complex pattern of viral RNA expression observed for these lymphoid cell lines can be interpreted in terms of recombination among three types of endogenous viral sequences: the Akv virus, a xenotropic virus, and an SL (for spontaneous leukemia) virus.     

Chimeric hepatitis B virus core particles as probes for studying peptide-integrin interactions.

An RGD-containing epitope from the foot-and-mouth disease virus (FMDV) VP1 protein was inserted into the e1 loop of the hepatitis B virus core (HBc) protein. This chimeric protein was expressed at high levels in Escherichia coli and spontaneously assembled into virus-like particles which could be readily purified. These fusion particles elicited high levels of both enzyme-linked immunosorbent assay- and FMDV-neutralizing antibodies in guinea pigs. The chimeric particles bound specifically to cultured eukaryotic cells. Mutant particles carrying the tripeptide sequence RGE in place of RGD and the use of a competitive peptide, GRGDS, confirmed the critical involvement of the RGD sequence in this binding. The chimeric particles also bound to purified integrins, and inhibition by chain-specific anti-integrin monoclonal antibodies implicated alpha 5 beta 1 as a candidate cell receptor for both the chimeric particle and FMDV. Some serotypes of FMDV bound to beta 1 integrins in solid- phase assays, and the chimeric particles competed with FMDV for binding to susceptible eukaryotic cells. Thus, HBc particles may provide a simple, general system for exploring the interactions of specific peptide sequences with cellular receptors.     

Structure of the caudal neural tube in an ascidian larva: Vestiges of its possible evolutionary origin from a ciliated band

Ultrastructural analysis and differential immunocytochemical staining with two antitubulin monoclonal antibodies were used to reexamine the organization and development of the neural tube in the larva of an ascidian, Ciona intestinalis, in appraisal of a theory that the dorsal tubular nervous system of the chordates evolved from two halves of a ciliated band in an auricularia-like larva of the kind found in echinoderms and hemichordates. One of the antibodies stained cilia in the nervous system and elsewhere; the other reacted primarily with neuronal axons. The caudal neural tube consists of four rows of large ciliated ependymal-glial cells enclosing an axial neural canal into which their single cilia extend. Two ventrolateral nerve tracts, containing axons, arise in the posterior brain region and extend along the length of the caudal tube, partially surrounded by the ependymal cells. The nonnervous, ciliated, ependymal neural tube of the ascidian larva with its two associated nerve tracts survives as a primitive early condition that could result from a ciliated band transformation. Tissues in the distal-most part of the ascidian larval tail have cell lineage origins that indicate an evolutionary history different from those in the proximal majority of the tail. The ependymal cells in this presumed later addition to the tail are not ciliated, although all of the others in the caudal ependymal tube appear to be.     

Protective immune response against foot-and-mouth disease.

The causative agents of foot-and-mouth disease (FMD) are small icosahedral viruses of the Aphthovirus group within the Picornaviridae family. There is no evidence that these viruses infect cells of the immune system or otherwise interfere detrimentally with their function; additionally, it has not been possible to relate cytotoxicity reactions against virus-infected cells to the efficacy of the immune response against FMD virus infection. In contrast, there is a close association between FMD virus antibody and the protective immune response (10, 14, 15, 20, 24, 25, 29-32). Induction of this antibody is dependent on the structure of the viral antigenic sites (7-9, 11, 18) and on the concomitant presence of Th-lymphocyte epitopes (4, 5, 7, 8), although a Th-lymphocyte-independent response has been reported (2). Recent work by Piatti et al. (26) showed that the immune response induced by FMD virus was only Th-lymphocyte dependent when low doses of antigen were used. This latter work was performed in mice, and it is not certain that a similar situation would be found in cattle. As for the major effector immune defense, this relies on the interaction between antibody-virus complexes and the phagocytic cells of the reticuloendothelial system (17, 19).     

Evaluation of the use of chromogenic and fluorogenic substrates in solid-phase enzyme linked immunosorbent assays (ELISA)

Fluorogenic and chromogenic substrates were used in direct and trapping enzyme-linked immunosorbent assays (ELISA) for the detection of mouse IgG and foot-and-mouth disease virus (FMDV). The detection limits for both antigens were compared using different combinations of enzymes and substrates. Various times and concentrations of chemicals were used to obtain maximum sensitivity for both systems. Similar sensitivities were found using fluorogenic and chromogenic substrates. Tetramethyl benzidine substrate for horse-radish peroxidase enzyme conjugates was found to attain the highest sensitivity levels for chromogenic assays (0.12 ng IgG/ml and 1.0 ng/ml FMDV respectively), after 10 min incubation. Of the two fluorogenic enzyme/substrates studied, B-galactosidase was the most sensitive but required extended incubation times (2-3 h) as compared with chromogenic systems. Special microplates for fluoro-immunoassay (FIA) were compared with conventional microplates and no advantage was found to justify their use. An alkaline phosphatase anti-guinea-pig conjugate was used to confirm the equivalence of fluorogenic and chromogenic substrates in terms of sensitivity. A comparison of the amount of signal generated using various concentrations of enzyme in the absence of antigen was made for two different alkaline phosphatase conjugates to obtain theoretical sensitivity limits. One possible advantage of fluorogenic substrates is that high binding ratio can improve the confidence in discrimination of positive results.