A molecular docking-based comparative assessment of various anticholinergic drugs as antidotes to different nerve agent poisoning.

Nerve agent poisoning is still a threat to civilization. Nerve agents function by binding with the enzyme acetylcholinesterase irreversibly. Accumulation of acetylcholine in the synapse causes over-stimulation of muscarinic and nicotinic acetylcholinergic receptors. Thus miosis, glandular hyper secretion, bronchoconstriction, vomiting, diarrhea and bradycardia occurs (by M1-M5 receptors stimulation); whereas convulsion and seizures occur due to the nicotinic receptors. Atropine is a non-selective muscarinic antagonists but no nicotinic antagonists are known. Seizures are controlled by diazepam. Enzyme aging occurs without treatment which causes the enzyme resistant to oxime therapy. Though numerous wet-lab based works has carried out, however, recent time there is an over-growing trend to make comparative assessment of drugs and toxicants. Here we made a molecular docking based comparative assessments between nerve agents toxicity and efficacy of different drugs to prevent this toxicity. Our results suggest that VX is the most harmful organophosphate nerve agents and HI-6 is the best drug followed by Obidoxime and Pralidoxime to free acetylcholinestarase. Docking results correspond the data trend of different in vivo experiments for the assessment of severity of different nerve agents and/or effectiveness of different antidote drugs. Our study reinforces the utility of pretreatment of the enzyme with a carbamic acid derivative like Pyridostigmine bromide which inhibits the enzyme reversibly to a smaller extent and thus, prevent the enzyme from aging and the nerve agent binding.Communicated by Ramaswamy H. Sarma.

Development of a Fast Fourier Transform-based Analytical Method for COVID-19 Diagnosis from Chest X-Ray Images Using GNU Octave.

Purpose: Many artificial intelligence-based computational procedures are developed to diagnose COVID-19 infection from chest X-ray (CXR) images, as diagnosis by CXR imaging is less time consuming and economically cheap compared to other detection procedures. Due to unavailability of skilled computer professionals and high computer architectural resource, majority of the employed methods are difficult to implement in rural and poor economic settings. Majority of such reports are devoid of codes and ignores related diseases (pneumonia). The absence of codes makes limitation in applying them widely. Hence, validation testing followed by evidence-based medical practice is difficult. The present work was aimed to develop a simple method that requires a less computational expertise and minimal level of computer resource, but with statistical inference. Materials and Methods: A Fast Fourier Transform-based (FFT) method was developed with GNU Octave, a free and open-source platform. This was employed to the images of CXR for further analysis. For statistical inference, two variables, i.e., the highest peak and number of peaks in the FFT distribution plot were considered. Results: The comparison of mean values among different groups (normal, COVID-19, viral, and bacterial pneumonia [BP]) showed statistical significance, especially when compared to normal, except between viral and BP groups. Conclusion: Parametric statistical inference from our result showed high level of significance (P < 0.001). This is comparable to the available artificial intelligence-based methods (where accuracy is about 94%). Developed method is easy, availability with codes, and requires a minimal level of computer resource and can be tested with a small sample size in different demography, and hence, be implemented in a poor socioeconomic setting.

A passage through systems biology to systems medicine: adoption of middle-out rational approaches towards the understanding of therapeutic outcomes in cancer.

During the last few decades, conventional practices in medicine including oncology focus their interests towards the reductionism of molecular detailing and at the analytical level population-based assessment with stochastic principles, technically called 'evidence-based medicine', is generally practiced. Due to fluctuations in physiological parameters, the analysis and prediction of a therapeutic outcome in cancer on an individual level is uncertain. In recent times the well accepted opinion is that cancer should be looked upon as a systems disorder. This makes a paradigm shift - from a fragmented to a systems approach, linear to nonlinear methodology and from genome to physiome based analysis to understand the cancer. In the arena of systems biology, different groups have different views, namely, bottom-up (mechanistic), top-down (operational) and middle-out (rational). With respect to cancer each has a special relevance to serve the specific objectivity. In this article we have reviewed the views of the different schools, recent developments and controversies associated with the uncertainties in prediction of the therapeutic outcome of cancer. Recent advances in dynamical science and control theory may provide suitable analytical tools for capturing the uncertainties associated with cancer therapy through the development of middle-out rationalist (MORA) views.

Computational molecular docking assessment of hormone receptor adjuvant drugs: Breast cancer as an example.

For the maintenance therapy of breast cancer, drugs which act as antagonists/partial agonists of hormone receptors against the breast tissue are used in the conventional clinical practices. However, during the course of treatment the patients may encounter systems related complications. Drugs like tamoxifen, which block the action of estrogens at its receptors in mammary gland; and the recently designed antiestrogens and selective estrogen receptor modulators (SERM) like raloxifene, toremifene and the progesterone antagonist mifepristone (RU-486) are used in the treatment for estrogen and/or progesterone receptor positive breast tumors. These drugs show, however, both acute and long-term toxicity like endometrial hyperplasia and cancer, menopausal symptoms, edema, thromboembolic events like pulmonary embolism and so on. Using molecular docking method, we studied the binding of these drugs at an array of receptors present within the physiological system. In addition, the molecular basis of the antiglucocorticoid and antiandrogenic side effects of mifepristone have also been studied. Our results show weak to moderate binding of these drugs at various receptors of the body. This may explain the toxicity and pathophysiological shifting by these drugs during the long term use of these drugs.

Mathematical modelling for the assessment of the effect of drug application delays in metronomic chemotherapy of cancer due to physiological constraints.

Several anti-angiogenic drugs in metronomic chemotherapy (MCT) scheduling in cancer have the potentiality to kill cancer cells. Theoretical analysis and experimental models have substantially indicated this potentiality. Therefore MCT may provide an option to improve the quality of life (QoL) with a quite reduced level of toxicity in the patient concerned. However, the criticism regarding MCT is that this may have a different toxicity profiling. This may require frequent interventions in the long drawn-out treatment schedule. Hence, it is worthwhile to devise a reliable estimation technique. Mathematical modelling and computer simulation techniques can assist in this regard. This, in turn, may help in the drug application decision. It is particularly important in situations where a fluctuating clearance rate of the applied drug is present. So, from dynamical perspectives, the frequencies and timings of drug stoppages need to be determined appropriately for maintaining the stability of the system without overburdening the toxicity level. Present work addresses the issue of subsequent drug administration delays and arrives at bounds of system performance and explores the treatment response in presence of physiological constraints.

Red cell morphology in leukemia, hypoplastic anemia and myelodysplastic syndrome.

Leukemic patients of different classifications are associated with anemia. Such clinical conditions are often referred to as refractory anemia, paraoxymal nocturnal hemoglobinuria, hemolytic uremia and autoimmune hemolytic anemia, all of which could be categorized as the cancer cachexia. In the present work, we have studied the overall morphology of intact red cells in different leukemic patients along with patients of hypoplastic anemia (HPA) by scanning electron microscopy. We have also studied the ultrastructure of the red cell surface membranes by transmission electron microscopy. For all experiments, erythrocytes from normal individuals served as controls. We have shown direct evidence of the altered red cell (RBC) membrane morphology irrespective of the hemoglobin status of the patients which includes (1) presence of large central holes in RBCs of acute myeloid leukemia (AML), (2) presence of thorn- and horn-like structure in RBCs of acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) and (3) flaccid appearance of RBCs in chronic lymphocytic leukemia (CLL) patients. A mixture of the above mentioned structures were found in the red cells of patients suffering from myelodysplastic syndrome (MDS) and in case of patients of HPA the RBCs lost the normal biconcave structures. TEM studies revealed presence of pores with diameters ranging from 100 to 200nm on the RBC membrane surface of myeloid leukemia with AML being the most prominent among others. Such pathophysiological alterations of the RBC morphology in leukemic patients could be identified as characteristic signature of the onset of anemia associated with the disease.

Efficacy and Toxicity Assessment of Different Antibody Based Antiangiogenic Drugs by Computational Docking Method.

Bevacizumab and trastuzumab are two antibody based antiangiogenic drugs that are in clinical practice for the treatment of different cancers. Presently applications of these drugs are based on the empirical choice of clinical experts that follow towards population based clinical trials and, hence, their molecular efficacies in terms of quantitative estimates are not being explored. Moreover, different clinical trials with these drugs showed different toxicity symptoms in patients. Here, using molecular docking study, we made an attempt to reveal the molecular rationale regarding their efficacy and off-target toxicity. Though our study reinforces their antiangiogenic potentiality and, among the two, trastuzumab has much higher efficacy; however, this study also reveals that compared to bevacizumab, trastuzumab has higher toxicity effect, specially on the cardiovascular system. This study also reveals the molecular rationale of ocular dysfunction by antiangiogenic drugs. The molecular rationale of toxicity as revealed in this study may help in the judicious choice as well as therapeutic scheduling of these drugs in different cancers.

Analysis of human lymphocyte antigen class I expression in gastric cancer by reverse transcriptase-polymerase chain reaction.

Malignant cells have been reported to escape immune surveillance by modulation of human lymphocyte antigen (HLA) class Ia molecule and/or other accessory molecules like TAP (transporter associated with antigen processing) and beta2-M expression. Most of these reports, however, are based on immunohistochemistry techniques with polymorphic- or isotype-specific antibodies. In the present study, we have instead used a locus-specific reverse transcriptase-polymerase chain reaction-based approach to detect the transcriptional expression of HLA class Ia as well as accessory molecules in gastric cancer. Our results indicate that HLA class Ia transcript is totally absent in only approximately 9% of cancer cases. Locus-specific expression of HLA-A and -B could, however, be detected in approximately 54% cases, whereas HLA-C was expressed in most of the cancer tissues. Interestingly, in some cases where HLA class Ia expression was observed, TAP1 expression could not be detected. Furthermore, we also investigated the frequency of nonclassical or HLA class Ib expression for molecules such as HLA-E and -G. HLA-G transcript was absent in gastric tissues both in cancerous and autologous normal region, whereas HLA-E was observed in a number of gastric cancers. Altogether these selective locus-specific losses of HLA class I along with impaired expression of accessory molecules may explain the complex phenomena by which gastric tumors escape both cytotoxic T-lymphocyte- as well as natural killer cell-mediated immune defense.

Dynamical model for assessment of anti-angiogenic therapy of cancer.

Different experimental models have substantially established that the anti-angiogenic (AAG)group of drugs are able to control the growth of tumor mass by cutting down the nutritive supply to the cancer cells. The mechanism of action of this group of drugs acts on the cells of the vascular endothelium. Recently, different AAG drugs have been in clinical trials. Initial clinical trials showed that application of AAG drugs produced different sorts of toxicity in patients,so calibration of the doses and drug application schedules are very important at present.Hence, development of analytical models would definitely help in this respect, particularly atthe individual level. The analytical model presented here may help to make a judicious choice of drug doses and drug schedule to control the growth of the tumor system under the condition of malignancy.

Analysis of HLA class Ia transcripts in human leukaemias.

Several leukaemia-specific antigens have been discovered in the recent past, which raised the possibility for T-cell-based immunotherapy for leukaemia. However, failure of such approaches involving interleukin-2 and/or T-cell-based immunotherapy indicated the importance of investigation of the human leucocyte antigen (HLA) status of the haematopoietic malignant cells. Considerable number of reports indicate that both HLA class I and class II are down-regulated in different cases of leukaemias, enabling them to evade immuno-surveillance. However, locus-specific down-regulation in leukaemia has not been widely investigated, although majority of cytotoxic T lymphocyte (CTL) responses are modulated by HLA-A and HLA-B, whereas expression of only HLA-C is unable to block natural killer (NK)-cell-mediated cytotolysis. Therefore, using RT-PCR, we have investigated the HLA class I transcriptional expression in a locus-specific manner, along with HLA-associated accessory molecules beta2-microglobulin and transporter-associated antigen processing molecule (TAP1). Our data suggest that in several newly diagnosed untreated leukaemic patients, HLA-C and beta2-microglobulin are expressed, but not the locus HLA-A or -B. Moreover, TAP1 and beta2-microglobulin were observed to be down-regulated in a number of cases of leukaemia. Our flow cytometric analysis of HLA-ABC also indicates a decrease in mean fluorescent intensity but no complete loss in surface expression of HLA class Ia on the leukaemic cells. Therefore, the observed low surface expression of HLA-ABC may be due to the down-regulation of transcription of HLA-A or -B itself and/or transcriptional suppression of the accessory molecules.