Investigating phosphate structural replacements through computational and experimental approaches

Bioisosteric replacements are used in drug design during lead generation and optimization processes with the aim to replace one functional group of a known molecule by another while retaining biological activity. The reason to use bioisosteric replacements are typically to optimize bioavailability or reducing toxicity. Phosphate groups represent a paradigm to study bioisosteric replacements. Protein-phosphate interaction plays a critical role during molecular recognition processes, and for example kinases represent one of the largest families of drug targets. However, some challenges exclude phosphate as a promising lead-like building block: i) charged phosphates do not cross molecular membranes; ii) some widely expressed proteins such as phosphatases easily hydrolyze phosphoric acid esters, which lead phosphate-containing ligands to lose their binding affinities before reaching their biological targets; iii) introduction of phosphate groups to parent scaffold is not easy. In the first part of the thesis work, I designed and implemented a computational protocol to mine information about phosphate structural replacements deposited in the Protein Data Bank. I constructed 116, 314, 271, and 42 sets of superimposed proteins where each set contains a reference protein to either POP, AMP, ADP, or ATP as well as a certain number of non-nucleotide ligands. 929 of such ligands are under study. The chemotypes that came out as structural replacements are diverse, ranging from common phosphate isosteres such as carboxyl, amide and squaramide to more surprising moieties such as benzoxaborole and aromatic ring systems. I exemplified some novel examples and interpreted the mechanism behind them. Local structural replacements are circumstance dependent: one chemical group valid in certain set-up cannot necessarily guarantee the success of another. The data from the study is available at http://86.50.168.121/phosphates_LSR.php. In the second part, I synthesized fifteen compounds retaining the adenosine moieties and bearing bioisosteric replacements of the phosphate at the ribose 5'-oxygen to test their stability toward human macro domain protein 1. These compounds are composed of either a squaryldiamide or an amide group as the bioisosteric replacement and/or as a linker. To these groups a variety of substituents were attached: phenyl, benzyl, pyridyl, carboxyl, hydroxy and tetrazolyl. Biological evaluation using differential scanning fluorimetry showed that four compounds stabilized human MDO1 at levels comparable to ADP and one at level comparable to AMP. Virtual screening was also run to identify MDO1 binding ligands. Among 20,000 FIMM database lead-like molecules, 39 compounds were selected for testing and eleven compounds found active based on ADPr and Poly-ADPr competition binding assay. The assay is however not well validated and a second confirmatory assay was conducted using calorimetry. To the best of my knowledge, this is the first report of non-endogenous ligands of the human MDO1. Altogether, this thesis highlights the versatility of molecular recognition processes that accompanies chemical replacements in compounds; this in turns shows the limits of the concepts of molecular similarity and classical bioisosterism that are based on the conservation of molecular interactions.Bioisosteeristä korvausta käytetään lääkeainekehityksessä johtolankamolekyylien tuottamisessa ja optimoinnissa. Tarkoitus on vaihtaa molekyylin funktionaalinen ryhmä toiseksi biologisen aktiivisuuden muuttumatta. Yleensä tavoitteena on parantaa biologista hyötyosuutta tai vähentää toksisuutta. Fosfaattiryhmää on tässä työssä käytetty esimerkkiryhmänä bioisosteerisiä korvauksia tutkittaessa. Väitöskirjatyön ensimmäisessä osassa suunnittelin ja toteutin tiedonlouhintaprotokollan etsiäkseni Protein Data Bank -tietokannasta korvaavia rakenteita fosfaattiryhmälle. Kokosin 116, 314, 271 ja 42 proteiiniryhmää, joissa kussakin on vertailumolekyylinä fosfaattiryhmän sisältävä POP, AMP, ADP tai ATP, ja lisäksi ei-nukleotidisiä ligandeja. Yhteensä 929 ei-nukleotidistä ligandia tutkittiin. Niistä löydettiin monipuolisesti fosfaattiryhmän korvaavia rakenteita, muun muassa yleisesti tunnettuja fosfaatin bioisosteerejä kuten karboksyyli, amidi ja squaramidi, mutta myös erikoisempia ryhmiä kuten bentsoksaboroli ja aromaattisia rengasrakenteita. Työssäni esittelen muutamia uusia rakenteita ja tulkitsen niiden vaikutusmekanismeja. Rakenteiden korvaaminen riippuu tilanteesta; yhteen tapaukseen sopiva korvaava ryhmä ei välttämättä toimi toisessa. Työn toisessa osassa syntetisoin 15 adenosiiniyhdistettä, joiden riboosiosan 5'-hapessa oleva fosfaattiryhmä on korvattu vaihtelevalla bioisosteerisellä ryhmällä. Bioisosteerisenä ryhmänä tai linkkerinä oli joko squaramidi- tai amidiryhmä. Yhdisteiden vakaus testattiin ihmisen MDO1-makrodomeeniproteiinin kanssa.Julkaisussa virheellinen verkkoaineiston ISBN 978-951-51-0045-0

Nanoparticulation of Prodrug into Medicines for Cancer Therapy

This article provides a broad spectrum about the nanoprodrug fabrication advances co-driven by prodrug and nanotechnology development to potentiate cancer treatment. The nanoprodrug inherits the features of both prodrug concept and nanomedicine know-how, attempts to solve underexploited challenge in cancer treatment cooperatively. Prodrugs can release bioactive drugs on-demand at specific sites to reduce systemic toxicity, this is done by using the special properties of the tumor microenvironment, such as pH value, glutathione concentration, and specific overexpressed enzymes; or by using exogenous stimulation, such as light, heat, and ultrasound. The nanotechnology, manipulating the matter within nanoscale, has high relevance to certain biological conditions, and has been widely utilized in cancer therapy. Together, the marriage of prodrug strategy which shield the side effects of parent drug and nanotechnology with pinpoint delivery capability has conceived highly camouflaged Trojan horse to maneuver cancerous threats

Endovascular Metal Devices for the Treatment of Cerebrovascular Diseases

Cerebrovascular disease involves various medical disorders that obstruct brain blood vessels or deteriorate cerebral circulation, resulting in ischemic or hemorrhagic stroke. Nowadays, platinum coils with or without biological modification have become routine embolization devices to reduce the risk of cerebral aneurysm bleeding. Additionally, many intracranial stents, flow diverters, and stent retrievers have been invented with uniquely designed structures. To accelerate the translation of these devices into clinical usage, an in‐depth understanding of the mechanical and material performance of these metal‐based devices is critical. However, considering the more distal location and tortuous anatomic characteristics of cerebral arteries, present devices still risk failing to arrive at target lesions. Consequently, more flexible endovascular devices and novel designs are under urgent demand to overcome the deficiencies of existing devices. Herein, the pros and cons of the current structural designs are discussed when these devices are applied to the treatment of diseases ranging broadly from hemorrhages to ischemic strokes, in order to encourage further development of such kind of devices and investigation of their use in the clinic. Moreover, novel biodegradable materials and drug elution techniques, and the design, safety, and efficacy of personalized devices for further clinical applications in cerebral vasculature are discussed.Peer reviewe

Macrodomain binding compound MRS 2578 inhibits alphavirus replication

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Macrodomain binding compound MRS 2578 inhibits alphavirus replication

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