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  • 1. Aeluri, Madhu
    et al.
    Gaddam, Jagan
    Trinath, Devarakonda V. K. S.
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska institutet.
    Arya, Prabhat
    An Intramolecular Heck Approach To Obtain 17-Membered Macrocyclic Diversity and the Identification of an Antiangiogenesis Agent from a Zebrafish Assay2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 19, p. 3955-3958Article in journal (Refereed)
    Abstract [en]

    We report a practical and modular approach to obtain two different types of 17-membered ring macrocyclic compounds through an intramolecular Heck reaction. These macrocyclic compounds are functionalized, that is, they contain two contiguous stereogenic hydroxy functional groups and an amino acid moiety in the macrocyclic ring skeleton. The macrocycles were then screened against a zebrafish assay to determine the antiangiogenesis activity of these small molecules. Macrocyclic compound 2.2a was identified as a potent inhibitor at 2.5 M, whereas its acyclic precursor and the other related macrocyclic compounds did not show any effect.

  • 2. Aeluri, Madhu
    et al.
    Pramanik, Chinmoy
    Chetia, Lakshindra
    Mallurwar, Naveen Kumar
    Balasubramanian, Sridhar
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institute.
    Arya, Prabhat
    14-Membered Macrocyclic Ring-Derived Toolbox: The Identification of Small Molecule Inhibitors of Angiogenesis and Early Embryo Development in Zebrafish Assay2013In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 15, no 3, p. 436-439Article in journal (Other academic)
    Abstract [en]

    A highly practical and modular synthesis to obtain a diverse 14-membered ring-based macrocyclic toolbox is achieved. These compounds were further tested in zebrafish assays related to early embryonic development, angiogenesis, and neurogenesis, respectively. 1.4c was Identified as an antiangiogenesis agent.

  • 3. Chamakuri, Srinivas
    et al.
    Guduru, Shiva Krishna Reddy
    Pamu, Sreedhar
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska institutet.
    Arya, Prabhat
    A Modular Approach to Build Macrocyclic Diversity in Aminoindoline Scaffolds Identifies Antiangiogenesis Agents from a Zebrafish Assay2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 19, p. 3959-3964Article in journal (Refereed)
    Abstract [en]

    A modular approach to explore the macrocyclic chemical space around an aminoindoline scaffold is developed. This is achieved by incorporating an amino acid moiety and subsequent stitching technology. Through screening of a zebrafish assay, several antiangiogenesis agents are identified.

  • 4. Dasari, Bhanudas
    et al.
    Jogula, Srinivas
    Borhade, Ramdas
    Balasubramanian, Sridhar
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institute.
    Arya, Prabhat
    Macrocyclic Glycohybrid Toolbox Identifies Novel Antiangiogenesis Agents from Zebrafish Assay2013In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 15, no 3, p. 432-435Article in journal (Other academic)
    Abstract [en]

    A practical and modular approach to obtain a diverse set of 14-membered macrocyclic compounds from carbohydrates is developed that utilizes functional groups at C-1 and C-5. The evaluation of this toolbox in various zebrafish assays led to the identification of 2.7f as an antianglogenesis agent.

  • 5. Guduru, Shiva Krishna Reddy
    et al.
    Chamakuri, Srinivas
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Arya, Prabhat
    Tetrahydroquinoline-Derived Macrocyclic Toolbox: The Discovery of Antiangiogenesis Agents in Zebrafish Assay2013In: ACS Medicinal Chemistry Letters, ISSN 1948-5875, E-ISSN 1948-5875, Vol. 4, no 7, p. 666-670Article in journal (Refereed)
    Abstract [en]

    A novel approach to incorporate the macrocyclic rings onto the privileged substructure, i.e. tetrahydroquinoline scaffold, is developed. The presence of an amino acid-derived moiety in the macrocyclic skeleton provides an opportunity to modulate the nature of the chiral side chain. Further, evaluation in a zebrafish screen identified three active small molecules (2.5b, 3.2d, and 4.2) as antiangiogenesis agents at 2.5 mu M.

  • 6.
    Hallgren, Stefan
    et al.
    Södertörn University College, School of Life Sciences.
    Kitambi, Satish Srinivas
    Karolinska Institutet.
    Cloning, sequencing and In situ localisation of guppy brain aromatase, cyp19bManuscript (preprint) (Other academic)
    Abstract [en]

    Oestrogens are biosynthesised by cytochrome p450-aromatase (Cyp19). Brain oestrogens serve several important functions of which nerve protection, cell proliferation, nerve development and behaviour control are a few. Teleost brain aromatase activity is exceptionally high (between 100-1000 times) compared to mammals and birds. We have successfully cloned and sequenced a 950 bp long partial fragment of the guppy CYP19B gene (PrCyp19b) derived from adult brain mRNA. Sequence alignment of translated amino acid sequence shows PrCYP19b having high sequence similarity to teleost brain aromatase. Anatomical distribution of PrCYP19b expression in adult guppy brains was studied using in situ-hybridisation with an antisense riboprobe synthesised from the cloned PrCYP19b gene. Expression of brain aromatase appeared at ventricular surfaces of the ventral telencephalic zones and the pre-optic area, in the hypothalamus, the pituitary gland, optic tectum and the cerebellum. This pattern is similar to previously reported distribution of brain aromatase in other teleosts. Measurement of brain aromatase activity in telencephalon, mesencephalon/diencephalon and rhombencephalon revealed female guppies producing the most oestrogens in mesencephalon/diencephalon, whereas males produces the most oestrogens in both telencephalon and mesencephalon/diencephalon. This indicates that brain oestrogen production is sexually dimorphic in the guppy and may serve different functions in the two genders.

  • 7. Jogula, Srinivas
    et al.
    Dasari, Bhanudas
    Khatravath, Mahender
    Chandrasekar, Gayathri
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska institutet.
    Arya, Prabhat
    Building a Macrocyclic Toolbox from C-Linked Carbohydrates Identifies Antiangiogenesis Agents from Zebrafish Assay2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 2013, no 23, p. 5036-5040Article in journal (Refereed)
    Abstract [en]

    We report the synthesis of four different types of macrocyclic-derived glycohybrids from carbohydrates that have an amino acid moiety in the large-ring skeleton. These macrocyclic glycohybrids were obtained from -C-1H- and -C-1H-linked carbohydrates. In one series, we utilized ring-closing metathesis as the stitching technology to obtain two different macrocycles, i.e., trans equatorial-axial C-1H and C-5H and cis axial-axial C-1H and C-5H. The click approach was the key reaction in our second series to obtain two other macrocyclic compounds, i.e., trans equatorial-axial C-1H and C-5H and cis axial-axial C-1H and C-5H. The evaluation of this toolbox resulted in the identification of two unique compounds as antiangiogenesis agents in an embryonic zebrafish assay. Interestingly, in both cases, the macrocyclic compounds that have a cis relationship (i.e., axial-axial orientation) between C-1H and C-5H showed activity and their other diastereomers (i.e., equatorial-axial C-1H and C-5 H) with a trans relationship did not show any effect.

  • 8.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Spatiotemporal Features of Neurogenesis in the Retina of Medaka, Oryzias latipes2008In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 237, no 12, p. 3870-3881Article in journal (Refereed)
    Abstract [en]

    The vertebrate retina is very well conserved in evolution. Its structure and functional features are very similar in phyla as different as primates and teleost fish. Here, we describe the spatiotemporal characteristics of neurogenesis in the retina of a teleost, medaka, and compare them with other species, primarily the zebrafish. Several intriguing differences are observed between medaka and zebrafish. For example, photoreceptor differentiation in the medaka retina starts independently in two different areas, and at more advanced stages of differentiation, medaka and zebrafish retinae display obviously different patterns of the photoreceptor cell mosaic. Medaka and zebrafish evolutionary lineages are thought to have separated from each other 110 million years ago, and so the differences between these species are not unexpected, and may be exploited to gain insight into the architecture of developmental pathways. Importantly, this work highlights the benefits of using multiple teleost models in parallel to understand a developmental process.

  • 9.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, USA.
    McCulloch, Kyle J.
    Harvard Medical School/MEEI, Boston, USA.
    Peterson, Randall T.
    Massachusetts General Hospital, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, USA.
    Small molecule screen for compounds that affect vascular development in the zebrafish retina2009In: Mechanisms of Development, ISSN 0925-4773, E-ISSN 1872-6356, Vol. 126, no 5-6, p. 464-477Article in journal (Refereed)
    Abstract [en]

    Blood vessel formation in the vertebrate eye is a precisely regulated process. in the human retina, both an excess and a deficiency of blood vessels may lead to a loss of vision. To gain insight into the molecular basis of vessel formation in the vertebrate retina and to develop pharmacological means of manipulating this process in a living organism, we further characterized the embryonic zebrafish eye vasculature, and performed a small molecule screen for compounds that affect blood vessel morphogenesis. The screening of approximately 2000 compounds revealed four small molecules that at specific concentrations affect retinal vessel morphology but do not produce obvious changes in trunk vessels, or in the neuronal architecture of the retina. Of these, two induce a pronounced widening of vessel diameter without a substantial loss of vessel number, one compound produces a loss of retinal blood vessels accompanied by a mild increase of their diameter, and finally one other generates a severe loss of retinal vessels. This work demonstrates the utility of zebrafish as a screening tool for small molecules that affect eye vasculature and presents several compounds of potential therapeutic importance.

  • 10.
    Kitambi, Satish Srinivas
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Teleost retina: a model for study neurogenesis and angiogenesis2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Teleost models, zebrafish and medaka have become popular models to study various aspects of developmental biology and genetics. The rapid embryonic development, transparent embryos and the availability of many mutants for various developmental and molecular pathways contribute to the usefulness of these models. The availability of various biochemical, molecular and genetic techniques applicable on these models facilitate in dissecting developmental processes. Teleost retina shows very high similarity to that seen in mammalian retina. The arrangement of the six types of neurons and one type of glia is very similar. Zebrafish has been extensively used in gaining insight into the development and functioning of the retina. Medaka, on the other hand has not been so extensively capitalized as zebrafish. The current study characterizes expression of genes mainly from the nuclear receptor family and establishes the role of zebrafish liver x receptor in governing the size, patterning and neurogenesis of the retina in zebrafish. We also establish the time line of the retinal patterning of medaka retina. Zebrafish and medaka retina show both similarity and difference in the developmental events governing the patterning of the retina. In zebrafish, retinal neurogenesis follows a fan gradient pattern starting at the ventro-nasal region. In medaka, neurogenesis starts from the central retina. An additional, second domain of neurogenesis is seen with the patterning of photoreceptors in medaka. This observation highlights the possibility of utilizing these two species as comparative models in gaining rapid understanding of retinal development and function. This study also establishes the time line of vascular development in the zebrafish retina, an important event required for normal function. Similar to neurogenesis, vasculaturedevelops rapidly and this feature was utilized to develop a small molecule-screening assay. The screening resulted in identification of five compounds that produced phenotype ranging from decrease in the number of vessels to loss of vessels specifically in the retina. To gain insight into the mode of action, further analyses of three of the five identified compounds, using either morpholino knockdown or structural similarity search was done. This study highlights the advantage of using zebrafish model to perform medically relevant chemical screen.

  • 11.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Archer, Amena
    Karolinska Institutet.
    Hallgren, Stefan
    Södertörn University, School of Life Sciences.
    Olsén, K Håkan
    Södertörn University, School of Life Sciences.
    Gustafsson, Åke
    Karolinska Institutet.
    Mode, Agneta
    Karolinska Institutet.
    The role of liver X receptor (lxr) in the developing eyeManuscript (preprint) (Other academic)
  • 12.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Chandrasekar, Gayathri
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Addanki, Vamsi Krishna
    Teleost fish - Powerful models for studying development, function and diseases of the human eye2011In: Current Science, ISSN 0011-3891, Vol. 100, no 12, p. 1815-1823Article in journal (Refereed)
    Abstract [en]

    The human eye is a highly specialized structure and defects in its development or functioning process have an impact on the quality of life. Different animal models, especially murine models, have been used to identify the key molecular players required for the normal functioning of the eye. This review highlights the importance of the teleost model in dissecting the development, functioning process and diseases of the human eye. A high degree of conservation is seen in the development, organization and function of the eye throughout vertebrates. Vertebrate teleost models, zebrafish and medaka, have become popular to study various aspects of developmental biology and genetics. Teleost eye shows high similarity to that of the mammalian eye; for example, as seen in mammals, the retina of zebrafish and medaka shows six types of neurons and one type of glia arranged in three layers. In addition, rapid embryonic development, transparency during early development, and the availability of various biochemical, molecular and genetic techniques applicable on these models facilitate in dissecting the developmental and functioning processes of the eye. The availability of mutants with eye defects in zebrafish and medaka allows the possibility of utilizing these two species as comparative models in gaining rapid understanding of the developmental events of various human diseases. The small size of these fish embryos and their availability in large numbers allow performing medically relevant chemical screens to identify potential drug and/or drug targets for different human eye conditions.

  • 13.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    The zebrafish orphan nuclear receptor genes nr2e1 and nr2e3 are expressed in developing eye and forebrain2007In: Gene Expression Patterns, ISSN 1567-133X, E-ISSN 1872-7298, Vol. 7, no 4, p. 521-528Article in journal (Refereed)
    Abstract [en]

    Mammalian Nr2e1 (Tailless, Mtll or Tlx) and Nr2e3 (photoreceptor-specific nuclear receptor, Pnr) are highly related orphan nuclear receptors, that are expressed in eye and forebrain-derived structures. In this study, we analyzed the developmental expression patterns of zebrafish nr2e1 and nr2e3. RT-PCR analysis showed that nr2e1 and nr2e3 are both expressed during embryonic and post-embryonic development. To examine the spatial distribution of nr2e1 and nr2e3 during development whole-mount in situ hybridization was performed. At tailbud stage, initial nr2e1 expression was localized to the rostral brain rudiment anterior to pax2.1 and eng2 expression at the prospective midbrain-hindbrain boundary. During Subsequent stages, nr2e1 became widely expressed in fore- and midbrain primordia, eye and olfactory placodes. At 24 hpf, strong nr2e1 expression was detected in telencephalon, hypothalamus, dorsal thalamus, pretectum, midbrain tectum, and retina. At 2 dpf, the initially widespread nr2e1 expression became more restricted to distinct regions within the fore- and midbrain and to the retinal ciliary margin, the germinal zone which gives rise to retina and presumptive iris. Express on of nr2e3 was exclusively found in the developing retina and epiphysis. In both structures, nr2e3 expression was found in photoreceptor cells. The developmental expression profile of zebrafish nr2e1 and nr2e3 is consistent with evolutionary conserved functions in eye and rostral brain structures.

  • 14. Srivastava, R.
    et al.
    Kitambi, Satish Srinivas
    Södertörn University, School of Life Sciences.
    Goyal, A.
    In silico analysis of thioredoxins and glutaredoxins2005In: Journal of Plant Biochemistry and Biotechnology, ISSN 0971-7811, E-ISSN 0974-1275, Vol. 14, no 2, p. 121-126Article in journal (Refereed)
    Abstract [en]

    Thioredoxins (TRXs) and glutaredoxins (GRXs) are ubiquitous small redox proteins belonging to the thioredoxin (TRX) superfamily. They regulate several cellular functions via mediating a dithiol/disulphide exchange in target proteins. Thioredoxins have been classified into several subgroups based on their structural homologs. In an attempt to identify thioredoxin proteins which have not been characterized, an EST database survey of Lycopersicon esculentum, Glycine max, Helianthus annus, Secale cereale, Solanum tuberosum, Apis mellifera ligustica, Oncorhynchus mykiss, Salmo salar, and whole genome survey for Drosophila melanogaster, Rattus norvegicus and Caenorhabditis briggsae was performed. Several glutaredoxin and glutaredoxin-like proteins from Ricinus communis, Vercinia fordii, Lycopersicon esculentum, Tilia platyphyllos, Populus tremuloides, Triticum aestivum and Oryza sativa were also characterized. The deduced amino acid sequences were aligned and phylogenetic trees were constructed to determine the consensus sequences and for establishing interrelationships amongst the new and established thioredoxin and glutaredoxins. Based on the alignments, proteins were designated to their respective classes and subcellular localization predictions were used to predict their possible site of actions. In silico analysis has identified several new thioredoxins, glutaredoxins and related proteins and provided insight into their evolutionary relationships.

  • 15. Srivastava, R.
    et al.
    Varshney, G. K.
    Kitambi, Satish Srinivas
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Amla, D. V.
    Analysis of glutamine synthetase (glnA) gene from prokaryotic and eukaryotic organisms2004In: Physiology and Molecular Biology of Plants, ISSN 0971-5894, Vol. 10, no 2, p. 197-202Article in journal (Refereed)
    Abstract [en]

    Glutamine synthetase (GS) is a key enzyme involved in nitrogen metabolism that performs the essential biochemical function of ammonium assimilation and glutamine synthesis. The enzyme and its isoforms are present universally in all organisms and display diverse regulatory patterns. In this study, we have analyzed some sequences upstream and downstream the initiation codon of the structural gene of GS (glnA) to show that these sequences are involved in regulation and stable expression of the enzyme. GS is known to be regulated by adenylylation-deadenylylation cascade in some organisms. Analysis of the adenylylation site from several organisms revealed that the site could also be deciphered from those organisms where regulation of the enzyme is not known by adenylylation. The adenylylation site was mutated by the use of Swiss-PdbViewer and possible reasons were assigned to the functional and nonfunctional properties of this site in various organisms. This analysis has also helped in assigning functional relationships to some conserved sequences within and in the proximity of the glnA gene.

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