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  • 51 Reads

Molecular docking of fructose-derived nucleoside analogs against reverse transcriptase of HIV-1

AIDS is a chronic infection that compromises the immune system of the individual infected with HIV, leaving him vulnerable to secondary infections. According to the Ministry of Health in 2017 there were 200,000 cases in Brazil, considered a worldwide pandemic with a record 36.7 million cases to date. HIV is a retrovirus, that is, it has RNA as a genetic material, and needs the action of reverse transcription (TR) to multiply. A nucleoside is formed by the N-glycosidic bond between a carbohydrate and a nitrogenous base (purine or pyrimidine) which in the biological medium is phosphorylated and inserted into the genetic material at the time of HIV viral multiplication. The bioactives analogous to the natural nucleosides upon being inserted by the TR into the DNA strand of an infected cell are not encoded and the retroviral multiplication process is immediately terminated by non-recognition of that analog. The major difficulty today is the action of these nucleoside analogs on other non-selective biological targets, such as the protease enzyme, and integrates, conferring toxicity to uninfected cells. This work consists of a computational analysis through Molecular Docking to predict the potential inhibitory activity of reverse transcriptase from a series of 24 nucleoside analogues derived from fructopyranose compared to the bioactive molecules already inserted in the anti-HIV treatment. For this study 36 molecules were designed in ChemDraw Ultra 12.0 to obtain its 2D structural formula. Then the molecule was optimized (RMS 0.1 kcal / Å.mol in maximum 660 cycles) by the Molecular Mechanics (MM +) and Semi-empirical (AM1) methods with the help of HyperChemTM (Release 8.0.6 for Windows) software for of the 3D structure. Finally, the enzyme reverse transcriptase in PBD (PDB ID 1REV) was selected and in Molegro Virtual Docking 6.0 anchorage was performed. Analyzing the results, it is possible to conclude that some molecules presented energies favorable to the formation of the ligand-enzyme complexes, as well as the presence of interactions with amino acid residues common to known inhibitors. Thus, this study contributes to obtaining new anti-HIV biomolecules through monosaccharides easily found in nature.

  • Open access
  • 52 Reads
A Machine Learning approach for the identification of CRISPR/Cas9 nuclease off-target for the treatment of Hemophilia

Hemophilia can be defined as a genetic disorder in which the body loses its capability to clot blood, and hence can’t stop blood flow. It is an X- linked recessive disease, hence mostly seen in males, with its severity significantly reduced in females. In India, hemophilia has an occurrence of 1 per 10,000 births, which generally progresses to a chronic disability or premature death in subjects left untreated or provided with suboptimal treatment, a case prevalent in India [1]. The two major types of this condition are hemophilia A or factor VIII deficiency and hemophilia B or factor IX deficiency. In addition, hemophilia C is a rare category in which inhibitory antibodies develop which show high affinity to procoagulants, thus neutralizing the effect of a coagulation factor. Inhibitors are much less common in patients with hemophilia B than in those with hemophilia A. The F8 gene present on the X chromosome is responsible for guiding the production of coagulation factor VIII, essential for forming blood clots. In hemophilia A, mutation results from two gross (140 kbp or 600 kbp) chromosomal inversions that involve introns 1 and 22, respectively. Similarly, the F9 gene present on the X chromosome mutates through several different mechanisms to give rise to hemophilia B condition. The conditions associated with hemophilia Leyden, ribosome readthrough of nonsense mutation and apparently ‘silent’ changes that do not alter amino acids are the major mutations studied. It has been observed that reconstitution with 1–2% of the clotting factor helps uplift the quality of life, while 5–20% reconstitution is required to ameliorate the genetic disorder. Gene-specific genome editing is preferred over random integration of expression cassettes as this helps avoid genotoxicity and achieve the required physiological levels of expression. Advances in genome engineering based on CRISPR- associated RNA- guided endonuclease Cas9 are empowering the guidance of the said endonuclease to target locations by a short RNA search string [2]. It requires a programmable sequence-specific RNA to direct it and introduce cleavage and double-stranded breaks at the target site. In case of hemophilia A, induced pluripotent stem cells (iPSCs) can be derived from patients with inversion genotypes with an aim to revert these chromosomal conditions to the corrected state with the assistance of CRISPR- Cas9 nucleases [3]. The endothelial cells from the corrected iPSCs can be checked for expression of F8 gene and the production of factor VIII. Likewise, in case of hemophilia B, delivery of naked Cas9-sgRNA plasmid and donor DNA, aiming to recover the mutation has shown a detectable gene correction (>1%) in F9 alleles of hepatocytes [4]. To construct the related plasmids, an AAVS1-Cas9-sgRNA plasmid is designed to cut the AAVSI locus in human. Subsequently, two donor plasmids are designed to insert GFP and F9 cDNA into the designated AAVS1 locus. Whole genome sequencing (WGS) is used in combination with this editing method to identify off-target mutations, to ensure that editing takes place at the desired site. The technique offers several benefits over the popularly used Adeno- associated viral (AAV) vectors such as precision, decreased insertional oncogenesis and control through an endogenous promoter [5]. The CRISPR/Cas9- mediated genome editing with an AAV8 vector has been put to use to provide an adjustable path to induce double-strand breaks at the target genes in hepatocytes [6]. The foremost need for CRISPR-Cas9 is the identification of targets that have undergone a mutation, which has led to the development of the said condition. Although a few targets are known, none of the target mutation has been capable to render a 5-20 percent of reconstitution that is required for the elimination of the disorder. Hence, there is a need to find novel targets for the CRISPR-Cas9 system, which in turn requires the assistance of computational tools. The aim of this study is to identify positive CRISPR-Cas9 targets which would help in better and more accurate treatment of the disorder with computational biology facilitating the research. The study provide targets which possess minimum off-target mutations, providing maximum reconstitution for hemophilia.


[1] Kar, A., Phadnis, S., Dharmarajan, S., & Nakade, J. (2014). Epidemiology & social costs of haemophilia in India. The Indian journal of medical research, 140(1), 19.

[2] Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6), 1262-1278.

[3] Park, C. Y., Kim, D. H., Son, J. S., Sung, J. J., Lee, J., Bae, S., ... & Kim, J. S. (2015). Functional correction of large factor VIII gene chromosomal inversions in hemophilia A patient-derived iPSCs using CRISPR-Cas9. Cell stem cell, 17(2), 213-220.

[4] Huai, C., Jia, C., Sun, R., Xu, P., Min, T., Wang, Q., ... & Lu, D. (2017). CRISPR/Cas9-mediated somatic and germline gene correction to restore hemostasis in hemophilia B mice. Human genetics, 136(7), 875-883.

[5] Doshi, B. S., & Arruda, V. R. (2018). Gene therapy for hemophilia: what does the future hold?.Therapeutic advances in hematology, 9(9), 273-293.

[6] Ohmori, T., Nagao, Y., Mizukami, H., Sakata, A., Muramatsu, S. I., Ozawa, K., ... & Sakata, Y. (2017). CRISPR/Cas9-mediated genome editing via postnatal administration of AAV vector cures haemophilia B mice. Scientific reports, 7(1), 4159.

  • Open access
  • 35 Reads
Machine learning models to predict the precise progression of Tay-Sachs and Related Disease


Tay Sachs is a very rare neurodegenerative disorder and the second most common lipid storage disorder. The testimony of TSD in infants is marked by the gradual loss in vision, hearing impairment, increased muscle stiffness and cherry red retinal spot. These symptoms progress to paralysis, dementia, seizures, neuro-regression leading to the demise of the patient by the age of 3 to 4 years of age. The neurological and visceral accumulation of glycosphingolipids accounts for the major morbidity and mortality of the patients [1]. Tay Sachs disorder (TSD) is characterised by the accumulation of the ganglioside in the brain nerve cells. The abnormal accumulation of the shpingolipids (GalNAc-&1,4-(NeuNAc-&2,3) -Gal+1,4-Glc_13-1,1{2-N-acyl) sphingosine and GalNAc-/3-1,4-Gal_P1,4- GlcQ- 1,1(2-N-acyl)sphingosine) in nerve tissue leads to progressive dysfunction of the central nervous system [2]. When the enzyme 3-N-acetyl hexosaminidase (hexosaminidase A (HEXA)) is responsible for the breakdown of the fats- are defective, the glycosphingolipids increase excessively.[3] The HEXA gene, responsible for coding of the hexosaminidase A, is located on Chromosome 15. Currently, there are no promising cure for TSD as the treatment targets the symptoms of the disease [4]. The advanced techniques have introduced CRISPR/cas9 as the suggestive treatment plan.

NGS (next generation sequencing) is one such diagnostic tool- providing rapid and accurate genomic information of the patient. The speculation of CRISPR/Cas9 requires critical understanding of the key genes involved, in order to design the treatment plan. The CRISPR (clustered regularly interspaced repeats) technology allows scientists to make the precise change in the genetic code. Cas9 endonucleases is the associated protein which is guided through specifically designed guide-RNA to the target DNA. CRISPR/Cas9 selectively target genes containing mutations that lead to non-functional products and correct the disease-causing mutations, in vitro and in vivo [5]. Currently the platforms used for gene editing for TSD patients include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and endonucleases. But these alternative platforms fail to provide ease and diversity in the areas where the CRISPR/cas9 excels. Owing to its ability to manipulate the target genes, however, the efficacy of the single guided RNA can be challenged, resulting in the unintended cleaving of the non-target sites. Thus, with the framework of the machine learning, using the algorithm of CRISTA the propensity of the cleaving the target site can be determined easily. The advanced techniques of machine learning along with NGS, provide varied scope of precise qualitative and quantitative study of the disorder.

The suggested research work holds promising and revolutionary grounds in designing the treatment plan for the patient. The precise treatment can be planned on the basis of early diagnosis of the disease. The development of machine learning techniques in this field can assure a definite neurotherapeutics as the models can predict the precise progression of disease. The proposed work not only provides the research in the area of Tay Sachs, but also pose to cure neurodegenerative disorders such as Alzheimer’s, dementia, Huntington’s, etc which still remain mystery to the scientists.


  1. Khera, D., John, J., Singh, K., & Faruq, M. (2018). Tay-Sachs disease: a novel mutation from India. BMJ Case Reports, 11(1), e225916. doi:10.1136/bcr-2018-225916
  2. Sandhoff, K. (1969). Variation of β‐N‐acetylhexosaminidase‐pattern in Tay‐Sachs disease. FEBS letters, 4(4), 351-354.
  3. (1998). Biochemical Pharmacology, 56(4), 421–430. doi:10.1016/s0006-2952(98)00115-4
  4. Kaback, M. (1993). Tay-Sachs Disease— Carrier Screening, Prenatal Diagnosis, and the Molecular Era. JAMA, 270(19), 2307. doi:10.1001/jama.1993.03510190063028
  5. Christensen, C., & Choy, F. (2017). A prospective treatment option for lysosomal storage diseases: CRISPR/Cas9 gene editing technology for mutation correction in induced pluripotent stem cells. Diseases, 5(1), 6.

  • Open access
  • 31 Reads
Seismic risk zonation using the geospatial tool: A case study over East and South district of Sikkim

Seismic risk assessment in the high mountains of Himalaya is necessary to
accommodate safe and suitable sites for homing with also to direct the pathway of plan and policy
for development sustainably. The continuous orogeny results often earthquakes, mostly, the area
around fault lines as have been documented by USGS. Hence, to prepare the vulnerability and
susceptible zonation in East and South Sikkim districts Analytical Hierarchy Process (AHP)
technique has been adopted. LANDSAT 8 onboard OLI multispectral data is used to prepare the
Land-use Land-cover map of study area using supervised classification techniques, while
CartoSAT-1 version 2 DEM is used to look into the physiographical aspects of this region. With
also, Geological Survey of India prepared soil and geological map is used to prepare the soil and
lineament map. Not only that, ground motion data of four different parameters, have also been
acquired form USGS on about of an earthquake event on 18th September 2011, which had
epicenter at 27.730°N, 88.155°E. Certainly, it has been achieved that, area with soil type of
udorthents entisol in the 10 km buffer zone from the major faults victimized of seismic hazard
mostly. By the AHP comparison matrix, proximity of any area to the fault lines found to be most
influential followed by the ground motion vectors while the LULC categories are the least
influential. Using the weighted overlay analysis, area along the western boundary of East district
and north-west of South district in Sikkim found to be under high seismic risk zone. Risk zones has
been verified with the help of archive earthquake data from USGS and approximately 22% area in
these two districts comes under high risk zone.

  • Open access
  • 31 Reads
Resveratrol as a possible multitarget drug for Alzheimer's Disease

Alzheimer's Disease is considered a multifactorial and really complex disorder. Pathological mechanisms in this illness are not completely identified and actual drugs have poor effects on disease's progression. Consequently, multi-target therapeutic turns attractive in the way to find new drug options. As a result of their antioxidant and anti-inflammatory benefits add to their regulation effects in signal transduction, apoptosis pathways, and cellular differentiation, polyphenols have an enormous value as chemoprotectors in SNC diseases. Resveratrol has multiple anti-AD effects including anti-inflammatory and anti-oxidant actions in neurodegeneration disorders, reduction of Aβ production and deposition, reduction of hyper phosphorylation of tau protein, regulation of mi RNA a gene translation, modulation of estrogen-dependent receptors, regulation of cell autophagy and neurotransmissor toxicity. Despite the pharmacokinetic challenges, resveratrol is a potential drug for a multi-target therapy model.

  • Open access
  • 4 Reads
Importance of HCN channels involved in various body conditions

HCN channels play a variety of important functions in our body, this can be from the control in the heart rate as in the central and peripheral nervous system. This type of channel is voltage dependent and has a permeability to Na+ and K+, this permeability is usually controlled by the cAMP that is inside the cell. HCN channels participate in human diseases such as pain, heart failure, etc., and having a fundamental role in our body functions can offer new tools that allow the pharmaceutical industry to develop drugs, mainly analgesics.

  • Open access
  • 14 Reads
Luciferase as a research technique for biological processes

Biolumiscence is the ability of some living beings to produce light thanks to chemical reactions in these organisms. The bioluminescence of fireflies has been used as an important tool (analytical techniques) within various studio fields. Luciferin (substrate for providing bioluminescence) is encoded by specific DNA sequences. Thanks to genetic engineering these sequences have been copied in such a way that they can be used in tissues for research purposes or for purposes such as cancer treatment. This article will talk about how light is formed from fireflies and how it is used in various applications.

  • Open access
  • 13 Reads
Medicinal plants extract for cancer treatment

Cancer is the leading cause of death worldwide, affecting child’s and adults, poor and rich, female and male. Between 30% and 50% of cancers type can be prevent with healthy lifestyle. On 2015, 8,8 million people died of cancer, this the 16% of world habitants. The economy impact of cancer is significant and still increasing. It is estimated that the total cost of cancer in 2010 was approximately of 1.16 billion dollars. Only one of five medium and low-income countries have necessary data to combat this illness. Nowadays, scientists are betting on herbal medicine for cancer and they are searching good results on this ancient’s treatments, increasing life expectancy of the patients.

  • Open access
  • 14 Reads
Use of Cannabis sativa L. for the treatment of Alzheimer's disease

Alzheimer´s Disease (AD) is a neurodegenerative disorder which represents a problem for the public health system because it affects more than 50 million people in the world, currently there is no successful treatment to treat this disease. The most accepted hypothesis regarding the development of this disease is the accumulation of plaques Aβ in the brain, have studied different molecules of natural origin as treatment based on this hypothesis. Cannabis sativa L. is a plant that has great potential as a treatment for this disease due to its antioxidant and neuroprotective properties and it has been shown to reduce the accumulation of Aβ plaques.

  • Open access
  • 28 Reads

Nanoemulsions as coadyuvants in intranasal vaccines

A considerable amount of human infections take place in mucous of the body, which is the reason why it is important to trigger immunological protection in this area. Even though parenteral administration of antigen induces efficient systemic protection, mucous from the body keep unprotected. Although attempts have been made to activate immunological protection in mucous membranes through different routes of application, some of them have had side effects or the desired effect has not been achieved clinically.

Nasal mucosa route has been studied for drug administration and for vaccines application in recent years using peptides/proteins or genetic structure materials. Among the advantages reported on this material, due to the nature of these ingredients, it is susceptible to enzymatic degradation processes, so its half-life is very short. In addition, they are not able to easily cross the mucous membranes of the body or the biological membranes. This led to the research and development of nanocarriers as coadyuvants, to protect these materials and give them more stability.

Research shows that mucosal vaccination has advantages over intramuscular immunization when it comes to provides mucosal protection, probably the most important of them is the fact that intranasal administration induces humoral and cellular immunity, which allows immunization at different mucosal sites as well as nasal mucosa, as well as systemic protection.