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Structure–activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase

Christina R. Bourne, Nancy Wakeham, Baskar Nammalwar, Vladimir Tseitin, Philip C. Bourne, Esther W. Barrow, Shankari Mylvaganam, Kal Ramnarayan, Richard A. Bunce, K. Darrell Berlin, William W. Barrow
<span title="2012-09-20">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zsupycdufvggvpoal5g3x5zi2a" style="color: black;">Biochimica et Biophysica Acta - Proteins and Proteomics</a> </i> &nbsp;
Bacterial resistance to antibiotic therapies is increasing and new treatment options are badly needed. There is an overlap between these resistant bacteria and organisms classified as likely bioterror weapons. For example, Bacillus anthracis is innately resistant to the anti-folate trimethoprim due to sequence changes found in the dihydrofolate reductase enzyme. Development of new inhibitors provides an opportunity to enhance the current arsenal of anti-folate antibiotics while also expanding
more &raquo; ... e coverage of the anti-folate class. We have characterized inhibitors of B. anthracis dihydrofolate reductase by measuring the K(i) and MIC values and calculating the energetics of binding. This series contains a core diaminopyrimidine ring, a central dimethoxybenzyl ring, and a dihydrophthalazine moiety. We have altered the chemical groups extended from a chiral center on the dihydropyridazine ring of the phthalazine moiety. The interactions for the most potent compounds were visualized by X-ray structure determination. We find that the potency of individual enantiomers is divergent with clear preference for the S-enantiomer, while maintaining a high conservation of contacts within the binding site. The preference for enantiomers seems to be predicated largely by differential interactions with protein residues Leu29, Gln30 and Arg53. These studies have clarified the activity of modifications and of individual enantiomers, and highlighted the role of the less-active R-enantiomer in effectively diluting the more active S-enantiomer in racemic solutions. This directly contributes to the development of new antimicrobials, combating trimethoprim resistance, and treatment options for potential bioterrorism agents.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbapap.2012.09.001">doi:10.1016/j.bbapap.2012.09.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22999981">pmid:22999981</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3530638/">pmcid:PMC3530638</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7cgoicumxfbaral7xz4izcbdwa">fatcat:7cgoicumxfbaral7xz4izcbdwa</a> </span>
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Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

Vsevolod Katritch, Chelsea M. Byrd, Vladimir Tseitin, Dongcheng Dai, Eugene Raush, Maxim Totrov, Ruben Abagyan, Robert Jordan, Dennis E. Hruby
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
Essential for viral replication and highly conserved among poxviridae, the vaccinia virus I7L ubiquitin-like proteinase (ULP) is an attractive target for development of smallpox antiviral drugs. At the same time, the I7L proteinase exemplifies several interesting challenges from the rational drug design perspective. In the absence of a published I7L X-ray structure, we have built a detailed 3D model of the I7L ligand binding site (S2-S2 0 pocket) based on exceptionally high structural
more &raquo; ... on of this site in proteases of the ULP family. The accuracy and limitations of this model were assessed through comparative analysis of available X-ray structures of ULPs, as well as energy based conformational modeling. The 3D model of the I7L ligand binding site was used to perform covalent docking and VLS of a comprehensive library of about 230,000 available ketone and aldehyde compounds. Out of 456 predicted ligands, 97 inhibitors of I7L proteinase activity were confirmed in biochemical assays (*20% overall hit rate). These experimental results both validate our I7L ligand binding model and provide initial leads for rational optimization of poxvirus I7L proteinase inhibitors. Thus, fragments predicted to bind in the prime portion of the active site can be combined with fragments on non-prime side to yield compounds with improved activity and specificity. Abbreviations PI Protease inhibitor ULP Ubiquitin-like proteases SAR Structure-activity relationship VLS Virtual ligand screening ICM Molecular modeling package from Molsoft, LLC
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Page 6023 of Mathematical Reviews Vol. , Issue 2000h [page]

<span title="">2000</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
G 58016 Tseitin, G. S 03058 Tseng, Chien-Cheng 94011 Tseytin, Gregory S See Tseitin, G. S Tseytlin, Arkady A 81312 Tsinober, Arkady See * 76002 Tsitouras, Ch 37136 Tsuboi, Zengo 81091 Tsuchiya, T.  ...  A. 81182 . 05242 49011 05037,05044 See Tong, Yung Liang 60028 52008 49028 Tomiyama, Masato Ton, Bui An Tonchev, Vladimir D Tong, Y. L Tong, Yung Liang Topala, Oleg Torki, Mounir Torrea, J.  ... 
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A Study on Nice Open Covers in Constructive Analysis [article]

Tong Cheng, Zhihan Gao, Yuxin Ma, Yuhan Ning, Jianghao Xu
<span title="2020-09-30">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Heine Borel theorem tells us that a closed bounded subset of Euclidean space R is compact, but in constructive mathematics, Tseitin and Zaslavskii showed that the set of all constructive real numbers between  ...  We are thankful to Torhea for organizing this program and to Vladimir Chernov for supervising the research project, who in turn is very grateful to Viktor Chernov for the multiple discussions about the  ...  Main Theorem Tseitin and Zaslavskii [9, 10, 11] showed that the set of all CRN between 0 and 1 is not compact. That is to say, we cannot always find a finite sub-cover from its open cover.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2009.02727v2">arXiv:2009.02727v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jfeyifjfvjaq5ckhmvvag5dgf4">fatcat:jfeyifjfvjaq5ckhmvvag5dgf4</a> </span>
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Page 5862 of Mathematical Reviews Vol. , Issue 98I [page]

<span title="">1998</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Shilov], Some results on propositional dynamic logic with fixed points (323-332); Vladimir V.  ...  Tseitin], Associ- ation nets: an alternative formalization of common thinking (385— 398); Hongwei Xi, Simulating 7-expansions with #-reductions in the second-order polymorphic A-calculus (399-409); Rostislav  ... 
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Page 3603 of Mathematical Reviews Vol. , Issue 2000e [page]

<span title="">2000</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Tseitin], A formalization of reasoning not derived from standard predicate logic (291-317); Andrei Voronkov, Simultaneous rigid E-unification and other de- cision problems related to the Herbrand theorem  ...  Lakemeyer, On sensing and off-line interpreting in GOLOG (173-189); Yves Lespérance, Kenneth Tam and Michael Jenkin, Reactivity in a logic-based robot programming framework (extended version) (190-207); Vladimir  ... 
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Page 1376 of Mathematical Reviews Vol. , Issue 86c [page]

<span title="">1986</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Trybuta, Stanistaw AUTHOR INDEX 86c co, Se ears ee Tseitin, G. S. Tseitlin, A. A. . 81059,83031 Teenie; G. B. ........- Tseitlin, M. G. Tseytlin, A. A. See Tseitlin, A. A.  ...  Vel’ov, Vladimir M. .. Veltkamp, G. W. van de Ven, A. Veniaminov, S. S. Veni Madhavan, C. E. Venkata Satyanarayana, M. 81033 Ver Eecke, Paul . See «01007 Vereshchagin, N.  ... 
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First-Order Modular Logic Programs and their Conservative Extensions [article]

Amelia Harrison, Yuliya Lierler
<span title="2017-02-17">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Acknowledgments Many thanks to Joshua Irvin, Vladimir Lifschitz, and Miroslaw Truszczynski for useful discussions regarding ideas in this paper.  ...  For example, consider the broadly used Tseitin transformation.  ...  The resulting formula is of a new signature, but both of the conditions of the definition hold between the original formula and the result of Tseitin transformation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1608.02681v2">arXiv:1608.02681v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3un3d35nfvhifegfp47aioxj2u">fatcat:3un3d35nfvhifegfp47aioxj2u</a> </span>
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Exponential Lower Bounds and Separation for Query Rewriting [chapter]

Stanislav Kikot, Roman Kontchakov, Vladimir Podolskii, Michael Zakharyaschev
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
The construction proceeds in two steps: first, we represent the f n by polynomial-size CNFs (in a way similar to the Tseitin transformation [27] ), and then encode those CNFs in terms of OWL 2 QL query  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-31585-5_26">doi:10.1007/978-3-642-31585-5_26</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/puryktsjm5hhpajksljr6vpu4m">fatcat:puryktsjm5hhpajksljr6vpu4m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120712144421/http://www.dcs.bbk.ac.uk/~michael/ICALP.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/0c/060c83990c6c5f906ba419ed9d5a62f7d49049bf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-31585-5_26"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Practical Detection of Entropy Loss in Pseudo-Random Number Generators

Felix Dörre, Vladimir Klebanov
<span title="">2016</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rau5643b7ncwvh74y6p64hntle" style="color: black;">Proceedings of the 2016 ACM SIGSAC Conference on Computer and Communications Security - CCS&#39;16</a> </i> &nbsp;
The auxiliary variables aux are used to represent intermediate states and for the Tseitin encoding 7 . • sha1(a b c) denotes the hash of the concatenation of a, b and c.  ...  The schematic equality of bitvectors in (4) is, in reality, encoded on the individual bit level; for the inequality, Tseitin encoding is used to obtain an equisatisfiable formula in conjunctive normal  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2976749.2978369">doi:10.1145/2976749.2978369</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ccs/DorreK16.html">dblp:conf/ccs/DorreK16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s2um543wizdfbjqepzbwclhjou">fatcat:s2um543wizdfbjqepzbwclhjou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218100945/https://static.aminer.org/pdf/20170130/pdfs/ccs/gsovfb5r0tqd2ie1k6wx4nut3evnmcoq.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fd/8b/fd8b3f3610d2ff3c771a4982b2955409c3f31d5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2976749.2978369"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

What is answer set programming to propositional satisfiability

Yuliya Lierler
<span title="2016-12-16">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ldxybeeoybgrrpc5b5v6mqdwty" style="color: black;">Constraints</a> </i> &nbsp;
Acknowledgments We are grateful for discussions with Remi Brochenin, Marc Denecker, Vladimir Lifschitz, Marco Maratea, Cesare Tinelli, Mirek Truszczyński, and Peter Schüller on the topics related to the  ...  It is a special case of the Tseitin procedure [77] that efficiently transforms any given propositional formula to CNF form by adding new atoms corresponding to its subformulas.  ... 
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Mathematical works of Vladimir A. Uspensky: A commentary [article]

Alexander Shen
<span title="2021-07-02">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Vladimir Andreevich Uspensky [1930-2018] was one of the Soviet pioneers of the theory of computation and mathematical logic in general (and my teacher and thesis advisor).  ...  Semenov, Vladimir A.  ...  [43] Vladimir A. Uspensky and Valery Ye. Plisko, Review: Raymond M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2008.02773v2">arXiv:2008.02773v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uppb7xzswrhczctovo7pomu53m">fatcat:uppb7xzswrhczctovo7pomu53m</a> </span>
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The price of query rewriting in ontology-based data access

Georg Gottlob, Stanislav Kikot, Roman Kontchakov, Vladimir Podolskii, Thomas Schwentick, Michael Zakharyaschev
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/weoplee4x5anpi62cco5v4higa" style="color: black;">Artificial Intelligence</a> </i> &nbsp;
In this section, given a family of monotone Boolean functions f n in NP, we first encode them-via the Tseitin transformation [59]-by means of polynomial-size CNFs, which are used to construct a sequence  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artint.2014.04.004">doi:10.1016/j.artint.2014.04.004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7asnadpjxfhgrh7iknr4hmncdy">fatcat:7asnadpjxfhgrh7iknr4hmncdy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808105551/http://www.dcs.bbk.ac.uk/~kikot/papers/AIJ-final.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d6/27/d627789407f9a263ac7b40b73ad085e5efda81f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artint.2014.04.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Answer Set Programming Based on Propositional Satisfiability

Enrico Giunchiglia, Yuliya Lierler, Marco Maratea
<span title="2006-09-29">2006</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2ewief65xnegfh2slwulpgsnba" style="color: black;">Journal of automated reasoning</a> </i> &nbsp;
Acknowledgements We are grateful to Paolo Ferraris, Nicola Leone, Vladimir Lifschitz and the anonymous reviewers of this paper for their helpful comments and/or discussions on the subject of the paper;  ...  the "classical conversion" (which given a formula in negative normal form recursively distributes conjunctions over disjunctions), and the conversions based on "renaming", such as those described in (Tseitin  ... 
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Gödel's incompleteness theorem

Vladimir A. Uspensky
<span title="">1994</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
Tseitin. Example 2.  ...  Tseitin showed that this associative calculus does not have an equivalence recognition algorithm.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/0304-3975(94)90222-4">doi:10.1016/0304-3975(94)90222-4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xvnw5noszjgp5edv6shx6v7yta">fatcat:xvnw5noszjgp5edv6shx6v7yta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161026162730/http://lpcs.math.msu.su/~uspensky/bib/Uspensky_1994_TCS_Godels_incompleteness_theorem.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8b/b1/8bb14aa7f91fdd3b324b7d5b78e2eedf936d92bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/0304-3975(94)90222-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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