August 23, 2011

Papers & Patents

For near to 10 years, researchers and graduate students working at the DLab produced a variety of scientific contributions, usually in the form of ISI research articles or papers. More recently, some biotechnology applications also derived in patent applications (see bottom).

Research Highlights
Review here the most significant contributions of DLab during the past 10 years. Contributions range from protein engineering, computer-based drug design to mathematical models.

Research papers
The following is the complete list of ISI research articles as available at the PubMed library at the National Center for Biotechnology Information (NCBI).

  1. Graphlet Based Metrics for the Comparison of Gene Regulatory Networks. Martin AJ, Dominguez C, Contreras-Riquelme S, Holmes DS, Perez-Acle T. P. ONE. 2016 Oct 3. doi: 10.1371/journal.pone.0163497.
  2. Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32. Brennan MJ, Karcz J, Vaughn NR, Woolwine-Cunningham Y, DePriest AD, Escalona Y, Perez-Acle T, Skerrett IM. J Biol Chem. 2015 Jul 10;290(28):17074-84. doi: 10.1074/jbc.M115.650747. Epub 2015 May 12.
  3. Keratitis-ichthyosis-deafness syndrome-associated Cx26 mutants produce nonfunctional gap junctions but hyperactive hemichannels when co-expressed with wild type Cx43. García IE, Maripillán J, Jara O, Ceriani R, Palacios-Muñoz A, Ramachandran J, Olivero P, Perez-AcleT, González C, Sáez JC, Contreras JE, Martínez AD. J Invest Dermatol. 2015 May;135(5):1338-47. doi: 10.1038/jid.2015.20. Epub 2015 Jan 27.
  4. Similarities between the Binding Sites of SB-206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile. Möller-Acuña P, Contreras-Riquelme JS, Rojas-Fuentes C, Nuñez-Vivanco G, Alzate-Morales J, Iturriaga-Vásquez P, Arias HR, Reyes-Parada M. PLoS One. 2015 Aug 5;10(8):e0134444. doi: 10.1371/journal.pone.0134444. eCollection 2015.
  5. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights. Chetty S, Bhakat S, Martin AJ, Soliman ME. J Biomol Struct Dyn. 2015 Mar 27:1-17.
  6. Towards bio-silicon interfaces: formation of an ultra-thin self-hydrated artificial membrane composed of dipalmitoylphosphatidylcholine (DPPC) and chitosan deposited in high vacuum from the gas-phase. Retamal MJ, Cisternas MA, Gutierrez-Maldonado SE, Perez-Acle T, Seifert B, Busch M, Huber P, Volkmann UG. J Chem Phys. 2014 Sep 14;141(10):104201. doi: 10.1063/1.4894224.
  7. An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine. Bhakat S, Martin AJ, Soliman ME. Mol Biosyst. 2014 Aug;10(8):2215-28. doi: 10.1039/c4mb00253a.
  8. Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans. Abarca F, Gutierrez-Maldonado SE, Parada P, Martinez P, Maass A, Perez-Acle T. PeerJ. 2014 Aug 5;2:e457. doi: 10.7717/peerj.457. eCollection 2014.
  9. Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Araya-Secchi R, Perez-Acle T, Kang SG, Huynh T, Bernardin A, Escalona Y, Garate JA, Martínez AD, García IE, Sáez JC, Zhou R. Biophys J. 2014 Aug 5;107(3):599-612. doi: 10.1016/j.bpj.2014.05.037.
  10. On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations. Garate JA, Perez-Acle T, Oostenbrink C. Phys Chem Chem Phys. 2014 Mar 21;16(11):5119-28. doi: 10.1039/c3cp54554g.
  11. Critical role of the first transmembrane domain of Cx26 in regulating oligomerization and function. Jara O, Acuña R, García IE, Maripillán J, Figueroa V, Sáez JC, Araya-Secchi R, Lagos CF, Pérez-Acle T, Berthoud VM, Beyer EC, Martínez AD. Mol Biol Cell. 2012 Sep;23(17):3299-311. Epub 2012 Jul 11.
  12. Molecular dynamics study of the archaeal aquaporin AqpM. Araya-Secchi R, Garate JA, Holmes DS, Perez-Acle T. BMC Genomics. 2011 Dec 22;12 Suppl 4:S8. doi: 10.1186/1471-2164-12-S4-S8. Epub 2011 Dec 22.
  13. Molecular basis of ligand dissociation in ?-adrenergic receptors. González A, Perez-Acle T, Pardo L, Deupi X. PLoS One. 2011;6(9):e23815. doi: 10.1371/journal.pone.0023815. Epub 2011 Sep 7.
  14. Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione. Lagos CF, Araya-Secchi R, Thomas P, Pérez-Acle T, Tapia RA, Salas CO. J Mol Model. 2012 May;18(5):2055-64. doi: 10.1007/s00894-011-1224-z. Epub 2011 Sep 6.
  15. Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology. González-Nilo F, Pérez-Acle T, Guínez-Molinos S, Geraldo DA, Sandoval C, Yévenes A, Santos LS, Laurie VF, Mendoza H, Cachau RE. Biol Res. 2011;44(1):43-51. doi: 10.4067/S0716-97602011000100006. Epub 2011 May 11.
  16. Uniaxial magnetic anisotropy energy of Fe wires embedded in carbon nanotubes. Muñoz F, Mejía-López J, Pérez-Acle T, Romero AH. ACS Nano. 2010 May 25;4(5):2883-91. doi: 10.1021/nn901834z.
  17. Life-giving caspases: revealing new roles during mouse embryo preimplantation development. Busso D, Dominguez C, Perez-Acle T, Moreno RD. Int J Dev Biol. 2010;54(5):857-65. doi: 10.1387/ijdb.092921db.
  18. Calpain inhibitors prevent p38 MAPK activation and germ cell apoptosis after heat stress in pubertal rat testes. Lizama C, Lagos CF, Lagos-Cabré R, Cantuarias L, Rivera F, Huenchuñir P, Pérez-Acle T, Carrión F, Moreno RD. J Cell Physiol. 2009 Nov;221(2):296-305. doi: 10.1002/jcp.21868.
  19. Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation. Barría MI, González A, Vera-Otarola J, León U, Vollrath V, Marsac D, Monasterio O, Pérez-Acle T, Soza A, López-Lastra M. Nucleic Acids Res. 2009 Feb;37(3):957-71. doi: 10.1093/nar/gkn1022. Epub 2008 Dec 23.
  20. Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Lagos CF, Caballero J, Gonzalez-Nilo FD, David Pessoa-Mahana C, Perez-Acle T. Chem Biol Drug Des. 2008 Nov;72(5):360-9. doi: 10.1111/j.1747-0285.2008.00716.x.
  21. Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3. Engel EA, Girardi C, Escobar PF, Arredondo V, Domínguez C, Pérez-Acle T, Valenzuela PD. Virus Genes. 2008 Aug;37(1):110-8. doi: 10.1007/s11262-008-0241-1. Epub 2008 May 23.
  22. A novel adrenocorticotropin receptor mutation alters its structure and function, causing familial glucocorticoid deficiency. Artigas RA, Gonzalez A, Riquelme E, Carvajal CA, Cattani A, Martínez-Aguayo A, Kalergis AM, Pérez-Acle T, Fardella CE. J Clin Endocrinol Metab. 2008 Aug;93(8):3097-105. doi: 10.1210/jc.2008-0048. Epub 2008 May 20.
  23. Computational modeling study of functional microdomains in cannabinoid receptor type 1. Gonzalez A, Duran LS, Araya-Secchi R, Garate JA, Pessoa-Mahana CD, Lagos CF, Perez-Acle T. Bioorg Med Chem. 2008 Apr 15;16(8):4378-89. doi: 10.1016/j.bmc.2008.02.070. Epub 2008 Feb 26.
  24. Structure-function relationship between the tobamovirus TMV-Cg coat protein and the HR-like response. Ehrenfeld N, Gonzalez A, Cañón P, Medina C, Perez-Acle T, Arce-Johnson P. J Gen Virol. 2008 Mar;89(Pt 3):809-17. doi: 10.1099/vir.0.83355-0.
  25. An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum. Colombres M, Garate JA, Lagos CF, Araya-Secchi R, Norambuena P, Quiroz S, Larrondo L, Pérez-Acle T, Eyzaguirre J. J Comput Aided Mol Des. 2008 Jan;22(1):19-28. Epub 2007 Dec 1.
  26. The N-homologue LRR domain adopts a folding which explains the TMV-Cg-induced HR-like response in sensitive tobacco plants. Stange C, Matus JT, Domínguez C, Perez-Acle T, Arce-Johnson P. J Mol Graph Model. 2008 Jan;26(5):850-60. Epub 2007 Jun 2.
  27. New approaches for predicting protein retention time in hydrophobic interaction chromatography. Lienqueo ME, Mahn A, Navarro G, Salgado JC, Perez-Acle T, Rapaport I, Asenjo JA. J Mol Recognit. 2006 Jul-Aug;19(4):260-9. Review.
  28. Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis. Blanco F, Garretón V, Frey N, Dominguez C, Pérez-Acle T, Van der Straeten D, Jordana X, Holuigue L. Plant Mol Biol. 2005 Dec;59(6):927-44.
  29. Hantavirus Gc glycoprotein: evidence for a class II fusion protein. Tischler ND, Gonzalez A, Perez-Acle T, Rosemblatt M, Valenzuela PD. J Gen Virol. 2005 Nov;86(Pt 11):2937-47.
  30. Acetylcholinesterase-amyloid-beta-peptide interaction: effect of Congo Red and the role of the Wnt pathway. Inestrosa NC, Alvarez A, Dinamarca MC, Pérez-Acle T, Colombres M. Curr Alzheimer Res. 2005 Jul;2(3):301-6. Review.
  31. The nop gene from Phanerochaete chrysosporium encodes a peroxidase with novel structural features. Larrondo L, Gonzalez A, Perez Acle T, Cullen D, Vicuña R. Biophys Chem. 2005 Jul 1;116(2):167-73.
  32. Myricetin, quercetin and catechin-gallate inhibit glucose uptake in isolated rat adipocytes. Strobel P, Allard C, Perez-Acle T, Calderon R, Aldunate R, Leighton F. Biochem J. 2005 Mar 15;386(Pt 3):471-8.
  33. Two homozygous mutations in the 11 beta-hydroxysteroid dehydrogenase type 2 gene in a case of apparent mineralocorticoid excess. Carvajal CA, Gonzalez AA, Romero DG, González A, Mosso LM, Lagos ET, Hevia Mdel P, Rosati MP, Perez-Acle TO, Gomez-Sanchez CE, Montero JA, Fardella CE. J Clin Endocrinol Metab. 2003 Jun;88(6):2501-7.
Patent applications

Molecular design tools are very effective techniques to innovate at the molecular level. Applications range from Protein Engineering and Computer Based Drug Design, to the development of Nanobiotechnology devices. Recently, a collaborative research effort carried out by researchers at the DLab, resulted in the design, synthesis and biological evaluation of new inhibitory drugs against Calpain II. These efforts were recently summed up into the Chilean patent application number 744-2010.

  1. Chilean patent application number 744-2010 (INAPI)
    Derivative substituted-phenilsulfonamide compounds as calpain inhibitors, pharmaceutical compositions, useful for the treatment of calpain-associated diseases such as male infertility, testis torsion, varicocele, olygospermia, Alzheimer disease, Parkinson disease, Huntignton disease and AIDS
  2. U.S. Provisional Patent Application 62/037,027 (14 August 2014) patent application number 744-2010 (INAPI)
    Biosilicon nanointerface based on an artificial membrane system


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