Artem Cherkasov

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. ncbi request reprint Can 'Bacterial-Metabolite-Likeness' model improve odds of 'in silico' antibiotic discovery?
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Chem Inf Model 46:1214-22. 2006
  2. ncbi request reprint Characterization of a new class of androgen receptor antagonists with potential therapeutic application in advanced prostate cancer
    Huifang Li
    Corresponding Author Artem Cherkasov, Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia, Canada V6H 3Z6
    Mol Cancer Ther 12:2425-35. 2013
  3. doi request reprint Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus
    Artem Cherkasov
    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Proteome Res 10:1139-50. 2011
  4. ncbi request reprint Progressive docking: a hybrid QSAR/docking approach for accelerating in silico high throughput screening
    Artem Cherkasov
    Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia V5Z 3J5
    J Med Chem 49:7466-78. 2006
  5. ncbi request reprint Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, BC, V5Z 3J5, Canada
    Molecules 9:1034-52. 2004
  6. ncbi request reprint Large-scale survey for potentially targetable indels in bacterial and protozoan proteins
    Artem Cherkasov
    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Faculty of Medicine, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
    Proteins 62:371-80. 2006
  7. ncbi request reprint 'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Chem Inf Model 45:1842-53. 2005
  8. ncbi request reprint Successful in silico discovery of novel nonsteroidal ligands for human sex hormone binding globulin
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Heather Pavilion, 2733, Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Med Chem 48:3203-13. 2005
  9. ncbi request reprint Selective targeting of indel-inferred differences in spatial structures of highly homologous proteins
    Artem Cherkasov
    Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada
    Proteins 58:950-4. 2005
  10. doi request reprint An updated steroid benchmark set and its application in the discovery of novel nanomolar ligands of sex hormone-binding globulin
    Artem Cherkasov
    Prostate Centre at the Vancouver General Hospital, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Med Chem 51:2047-56. 2008

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Can 'Bacterial-Metabolite-Likeness' model improve odds of 'in silico' antibiotic discovery?
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Chem Inf Model 46:1214-22. 2006
    ..These results illustrate immanent similarity between conventional antimicrobials and native bacterial metabolites and suggest that the developed BML model can be an effective classification tool for 'in silico' antibiotic studies...
  2. ncbi request reprint Characterization of a new class of androgen receptor antagonists with potential therapeutic application in advanced prostate cancer
    Huifang Li
    Corresponding Author Artem Cherkasov, Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia, Canada V6H 3Z6
    Mol Cancer Ther 12:2425-35. 2013
    ..These results provide a foundation for the development of a new class of androgen receptor antagonists that can help address the problem of antiandrogen resistance in prostate cancer...
  3. doi request reprint Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus
    Artem Cherkasov
    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Proteome Res 10:1139-50. 2011
    ..Thus, this empirical MRSA-252 PIN provides a rich source for identifying critical proteins essential for network stability, many of which can be considered as prospective antimicrobial drug targets...
  4. ncbi request reprint Progressive docking: a hybrid QSAR/docking approach for accelerating in silico high throughput screening
    Artem Cherkasov
    Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia V5Z 3J5
    J Med Chem 49:7466-78. 2006
    ....
  5. ncbi request reprint Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, BC, V5Z 3J5, Canada
    Molecules 9:1034-52. 2004
    ..The developed approach can be further expanded for the larger sets of biologically active peptides and can serve as a useful quantitative tool for rational antibiotic design and discovery...
  6. ncbi request reprint Large-scale survey for potentially targetable indels in bacterial and protozoan proteins
    Artem Cherkasov
    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Faculty of Medicine, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
    Proteins 62:371-80. 2006
    ..The finding suggested that the occurrence of sequence indels may be involved in the evolution of pathogenic mechanisms in these protozoa...
  7. ncbi request reprint 'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Chem Inf Model 45:1842-53. 2005
    ..When the selected substances were evaluated for their ability to bind SHBG in vitro, three of them displaced testosterone from the SHBG steroid-binding site, and with one compound this was achieved at micromolar concentrations...
  8. ncbi request reprint Successful in silico discovery of novel nonsteroidal ligands for human sex hormone binding globulin
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Heather Pavilion, 2733, Heather Street, Vancouver, British Columbia V5Z 3J5, Canada
    J Med Chem 48:3203-13. 2005
    ..Taken together, the in silico strategy we have developed will aid in the discovery of nonsteroidal ligands of SHBG with novel pharmacological properties...
  9. ncbi request reprint Selective targeting of indel-inferred differences in spatial structures of highly homologous proteins
    Artem Cherkasov
    Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada
    Proteins 58:950-4. 2005
    ..These findings may establish a new strategy for the development of antagonists directed against certain pathogenic targets having close human homologues...
  10. doi request reprint An updated steroid benchmark set and its application in the discovery of novel nanomolar ligands of sex hormone-binding globulin
    Artem Cherkasov
    Prostate Centre at the Vancouver General Hospital, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Med Chem 51:2047-56. 2008
    ..The resulting QSAR models combined with CoMFA and CoMSiA models as well as structure-based virtual screening allowed discovering several low-micromolar to nanomolar nonsteroidal inhibitors for human SHBG...
  11. pmc Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:101. 2004
    ..For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment...
  12. pmc Structural characterization of genomes by large scale sequence-structure threading
    Artem Cherkasov
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:37. 2004
    ..Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes...
  13. pmc An approach to large scale identification of non-obvious structural similarities between proteins
    Artem Cherkasov
    Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
    BMC Bioinformatics 5:61. 2004
    ..When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy...
  14. ncbi request reprint QSAR modeling and computer-aided design of antimicrobial peptides
    Håvard Jenssen
    Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    J Pept Sci 14:110-4. 2008
    ....
  15. doi request reprint Cheminformatics-driven discovery of selective, nanomolar inhibitors for staphylococcal pyruvate kinase
    Peter Axerio-Cilies
    Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
    ACS Chem Biol 7:350-9. 2012
    ..Equally noteworthy, the results of the current work highlight the importance of rigorous cheminformatics-based exploration of the results of high-throughput experiments...
  16. doi request reprint In silico identification of anthropogenic chemicals as ligands of zebrafish sex hormone binding globulin
    Nels Thorsteinson
    Prostate Centre at the Vancouver General Hospital, University of British Columbia, BC, Canada
    Toxicol Appl Pharmacol 234:47-57. 2009
    ..Such studies could increase the awareness of hazards posed by existing commercial chemicals at relatively low cost...
  17. doi request reprint Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs
    Artem Cherkasov
    Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, British Columbia V6T 1Z3, Canada
    ACS Chem Biol 4:65-74. 2009
    ....
  18. ncbi request reprint Indel-based targeting of essential proteins in human pathogens that have close host orthologue(s): discovery of selective inhibitors for Leishmania donovani elongation factor-1alpha
    Devki Nandan
    Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    Proteins 67:53-64. 2007
    ..We anticipate that such indel-directed targeting of essential proteins in microbial pathogens may help address the growing problem of antibiotic resistance...
  19. ncbi request reprint Selective targeting of indel-inferred differences in spatial structures of homologous proteins
    Yvonne Y Li
    CIHR MSFHR Strategic Training Program in Bioinformatics, University of British Columbia, 570 West 7th Avenue, Vancouver, British Columbia, V5Z 4S6, Canada
    J Bioinform Comput Biol 4:403-14. 2006
    ..While experimental evidence is required to verify our results, our findings thus far appear to support this approach as a new strategy for the development of antagonists against pathogenic targets having close human homologs...
  20. doi request reprint Optimization of antibacterial peptides by genetic algorithms and cheminformatics
    Christopher D Fjell
    Faculty of Medicine, Division of Infectious Diseases, Department of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, BC, Canada
    Chem Biol Drug Des 77:48-56. 2011
    ..While GA significantly improves the possibility of identifying candidate peptides, we encountered important pitfalls to this method that should be considered when using GA...
  21. doi request reprint Identification of novel host defense peptides and the absence of alpha-defensins in the bovine genome
    Christopher D Fjell
    Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    Proteins 73:420-30. 2008
    ..Since we could find no technical reasons these would be missed and no references to bovine alpha-defensins in the literature, this suggests that cattle lack this important family of host defense peptides...
  22. doi request reprint Identification of novel antibacterial peptides by chemoinformatics and machine learning
    Christopher D Fjell
    Department of Medicine, Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Med Chem 52:2006-15. 2009
    ....
  23. ncbi request reprint Targeting the binding function 3 (BF3) site of the androgen receptor through virtual screening. 2. development of 2-((2-phenoxyethyl) thio)-1H-benzimidazole derivatives
    Ravi Shashi Nayana Munuganti
    Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
    J Med Chem 56:1136-48. 2013
    ..Some of the developed BF3 ligands demonstrated significant antiandrogen potency against LNCaP and Enzalutamide-resistant prostate cancer cell lines...
  24. pmc Targeting the binding function 3 (BF3) site of the human androgen receptor through virtual screening
    Nathan A Lack
    Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
    J Med Chem 54:8563-73. 2011
    ..These findings lay a foundation for the development of alternative or supplementary therapies capable of combating prostate cancer even in its antiandrogen resistant forms...
  25. pmc Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins
    Michael Hsing
    Bioinformatics Graduate Program, Faculty of Graduate Studies, University of British Columbia, 100 570 West 7th Avenue, Vancouver, BC V5T 4S6, Canada
    BMC Bioinformatics 9:293. 2008
    ..Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown...
  26. doi request reprint Towards improved assessment of functional similarity in large-scale screens: a study on indel length
    Alexander Schönhuth
    School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
    J Comput Biol 17:1-20. 2010
    ..Our method can be reliably employed to quickly filter alignment outputs for protein pairs that are more likely to be functionally similar and/or divergent and establishes a sound and useful add-on for large-scale alignment studies...
  27. doi request reprint Using molecular docking, 3D-QSAR, and cluster analysis for screening structurally diverse data sets of pharmacological interest
    Osvaldo A Santos-Filho
    Jack Bell Research Centre at Vancouver General Hospital, Faculty of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia, Canada
    J Chem Inf Model 48:2054-65. 2008
    ....
  28. ncbi request reprint Short linear cationic antimicrobial peptides: screening, optimizing, and prediction
    Kai Hilpert
    Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada
    Methods Mol Biol 494:127-59. 2008
    ..Inductive" QSAR in combination with more complex mathematical modeling algorithms such as artificial neural networks (ANNs) may yield powerful new methods for in silico identification of novel antimicrobial peptides...
  29. ncbi request reprint Molecular cloning, biochemical and structural analysis of elongation factor-1 alpha from Leishmania donovani: comparison with the mammalian homologue
    Devki Nandan
    Department of Medicine, Division of Infectious Diseases, Faculty of Medicine, The Research Institute of the Vancouver Hospital and Health Sciences Center, The University of British Columbia, Vancouver, BC, Canada V5Z 3J5
    Biochem Biophys Res Commun 302:646-52. 2003
    ..Since EF-1 alpha is essential for survival, the distinct biochemical and structural properties of Leishmania EF-1 alpha may provide a novel target for drug development...
  30. ncbi request reprint Molecular architecture of leishmania EF-1alpha reveals a novel site that may modulate protein translation: a possible target for drug development
    Martin Lopez
    Department of Medicine Division of Infectious Diseases, University of British Columbia, Faculties of Medicine and Science, 2733 Heather Street, Heather Pavilion East, Room 452 D, Vancouver, BC, Canada V5Z 3J5
    Biochem Biophys Res Commun 356:886-92. 2007
    ..Taken together, these findings identify a novel, exposed region in leishmania EF-1alpha that may be involved in protein synthesis and a potential site for drug targeting...
  31. doi request reprint Inhibitors of androgen receptor activation function-2 (AF2) site identified through virtual screening
    Peter Axerio-Cilies
    Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
    J Med Chem 54:6197-205. 2011
    ..Taken together, our results provide a promising ground for development of novel anti-androgens that can help to address the problem of drug resistance in prostate cancer...
  32. doi request reprint Identification of novel androgen receptor antagonists using structure- and ligand-based methods
    Huifang Li
    Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
    J Chem Inf Model 53:123-30. 2013
    ..These results set a ground for the development of novel classes of PCa drugs that are structurally different from current AR antagonists...
  33. pmc Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast
    Fiona S L Brinkman
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
    Genome Res 12:1159-67. 2002
    ....
  34. ncbi request reprint AMPer: a database and an automated discovery tool for antimicrobial peptides
    Christopher D Fjell
    Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 23:1148-55. 2007
    ..with up to 99% accuracy and can be used for discovering novel AMP candidates...
  35. pmc The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks
    Michael Hsing
    Faculty of Graduate Studies, Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
    BMC Syst Biol 2:80. 2008
    ..Thus, it is crucial to be able to identify hub proteins based not only on experimental data but also by means of bioinformatics predictions...
  36. pmc Modeling of cell signaling pathways in macrophages by semantic networks
    Michael Hsing
    CIHR MSFHR Strategic Training Program in Bioinformatics, Genetics Graduate Program, Faculty of Graduate Studies, University of British Columbia, Vancouver, British Columbia, V5Z 3J5, Canada
    BMC Bioinformatics 5:156. 2004
    ..Moreover, the critical knowledge of cause-effect relationships among signaling events is not reflected by most conventional approaches for manipulating pathways...
  37. pmc Relationship between insertion/deletion (indel) frequency of proteins and essentiality
    Simon K Chan
    CIHR MSFHR Strategic Training Program in Bioinformatics, Canada s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
    BMC Bioinformatics 8:227. 2007
    ..The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins...
  38. ncbi request reprint Distance based algorithms for small biomolecule classification and structural similarity search
    Emre Karakoc
    School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    Bioinformatics 22:e243-51. 2006
    ..The data structure for performing search should be very efficient as the molecular databases of interest include several millions of compounds...
  39. ncbi request reprint Evaluating different descriptors for model design of antimicrobial peptides with enhanced activity toward P. aeruginosa
    Håvard Jenssen
    Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Chem Biol Drug Des 70:134-42. 2007
    ..7 +/- 1.6 peptides. The model has also been proven significantly more accurate than a simpler model (Bac2a- #1), where the inductive and conventional quantitative structure-activity relationship descriptors were excluded...
  40. pmc Molecular analysis of the multiple GroEL proteins of Chlamydiae
    Karuna P Karunakaran
    University of British Columbia Centre for Disease Control Genome Sequence Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    J Bacteriol 185:1958-66. 2003
    ..coli groEL mutant. Complementation did not occur with groEL2 or groEL3 alone or together with groES. The role for each of the three GroELs in the chlamydial developmental cycle and in disease pathogenesis requires further study...
  41. pmc Luteolin is a novel p90 ribosomal S6 kinase (RSK) inhibitor that suppresses Notch4 signaling by blocking the activation of Y-box binding protein-1 (YB-1)
    Kristen M Reipas
    Laboratory for Oncogenomic Research, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
    Oncotarget 4:329-45. 2013
    ..In conclusion, inhibiting the RSK/YB-1 pathway with luteolin is a novel approach to blocking Notch4 signaling and as such provides a means of inhibiting TICs...
  42. pmc Identification of pyruvate kinase in methicillin-resistant Staphylococcus aureus as a novel antimicrobial drug target
    Roya Zoraghi
    Department of Medicine, Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
    Antimicrob Agents Chemother 55:2042-53. 2011
    ....
  43. doi request reprint The mycobacterial antibiotic resistance determinant WhiB7 acts as a transcriptional activator by binding the primary sigma factor SigA (RpoV)
    Ján Burian
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, Centre for Tuberculosis Research, University of British Columbia, Vancouver, Canada V6T 1Z3 and Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada V6T 1Z3
    Nucleic Acids Res 41:10062-76. 2013
    ..Inhibitors preventing WhiB7 interactions could allow the use of previously ineffective antibiotics for treatment of mycobacterial diseases. ..
  44. pmc A non-synonymous coding variant (L616F) in the TLR5 gene is potentially associated with Crohn's disease and influences responses to bacterial flagellin
    Jared Sheridan
    Division of Infectious Diseases, Vancouver Hospital and University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e61326. 2013
    ..We aimed to examine potential CD-associated TLR5 variants and assess whether they modified inflammatory responses to bacterial flagellins...
  45. ncbi request reprint A phosphorylation site in the Toll-like receptor 5 TIR domain is required for inflammatory signalling in response to flagellin
    Sabine M Ivison
    Division of Infectious Diseases, University of British Columbia Vancouver Coastal Health Research Institute, Canada
    Biochem Biophys Res Commun 352:936-41. 2007
    ..Together, these results suggest that phosphorylation of Y798 in TLR5 is required for signalling, but not for TLR5 dimerization...
  46. pmc Targeting alternative sites on the androgen receptor to treat castration-resistant prostate cancer
    Nada Lallous
    Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
    Int J Mol Sci 14:12496-519. 2013
    ..It is anticipated that these new classes of anti-AR drugs will provide an additional arsenal to treat castration-resistant prostate cancer...
  47. ncbi request reprint Comparative QSAR- and fragments distribution analysis of drugs, druglikes, metabolic substances, and antimicrobial compounds
    Emre Karakoc
    School of Computing Science, Simon Fraser University, Burnaby, Canada
    J Chem Inf Model 46:2167-82. 2006
    ....
  48. doi request reprint Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis
    Hao Zhu
    Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    J Chem Inf Model 48:766-84. 2008
    ....