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Items: 38

1.

Computational Study of Conformational Changes in Human 3-hydroxy-3-methylglutaryl Coenzyme Reductase Induced by Substrate Binding.

da Costa CHS, Oliveira ARS, Dos Santos AM, da Costa KS, E Lima AHL, Alves CN, Lameira J.

J Biomol Struct Dyn. 2018 Nov 23:1-26. doi: 10.1080/07391102.2018.1549508. [Epub ahead of print]

PMID:
30470158
2.

Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles.

Dos Santos AM, Cianni L, De Vita D, Rosini F, Leitão A, Laughton CA, Lameira J, Montanari CA.

Phys Chem Chem Phys. 2018 Sep 26;20(37):24317-24328. doi: 10.1039/c8cp03320j.

PMID:
30211406
3.

First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents.

Alencar N, Sola I, Linares M, Juárez-Jiménez J, Pont C, Viayna A, Vílchez D, Sampedro C, Abad P, Pérez-Benavente S, Lameira J, Bautista JM, Muñoz-Torrero D, Luque FJ.

Eur J Med Chem. 2018 Feb 25;146:108-122. doi: 10.1016/j.ejmech.2018.01.044. Epub 2018 Feb 4.

PMID:
29407943
4.

Computational analyses of interactions between ALK-5 and bioactive ligands: insights for the design of potential anticancer agents.

Almeida MO, Costa CHS, Gomes GC, Lameira J, Alves CN, Honorio KM.

J Biomol Struct Dyn. 2018 Nov;36(15):4010-4022. doi: 10.1080/07391102.2017.1404938. Epub 2017 Nov 28.

PMID:
29132261
5.

Structural and evolutionary analysis of Leishmania Alba proteins.

da Costa KS, Galúcio JMP, Leonardo ES, Cardoso G, Leal É, Conde G, Lameira J.

Mol Biochem Parasitol. 2017 Oct;217:23-31. doi: 10.1016/j.molbiopara.2017.08.006. Epub 2017 Aug 25.

PMID:
28847609
6.

Unraveling the Addition-Elimination Mechanism of EPSP Synthase through Computer Modeling.

Dos Santos AM, Lima AH, Alves CN, Lameira J.

J Phys Chem B. 2017 Sep 21;121(37):8626-8637. doi: 10.1021/acs.jpcb.7b05063. Epub 2017 Sep 8.

PMID:
28829128
7.

Catalysis by solvation rather than the desolvation effect: exploring the catalytic efficiency of SAM-dependent chlorinase.

Araújo E, Lima AH, Lameira J.

Phys Chem Chem Phys. 2017 Aug 16;19(32):21350-21356. doi: 10.1039/c7cp02811c.

PMID:
28762403
8.

Mycobacterium abscessus l,d-Transpeptidases Are Susceptible to Inactivation by Carbapenems and Cephalosporins but Not Penicillins.

Kumar P, Chauhan V, Silva JRA, Lameira J, d'Andrea FB, Li SG, Ginell SL, Freundlich JS, Alves CN, Bailey S, Cohen KA, Lamichhane G.

Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e00866-17. doi: 10.1128/AAC.00866-17. Print 2017 Oct.

9.

Inhibition of tyrosinase by 4H-chromene analogs: Synthesis, kinetic studies, and computational analysis.

Brasil EM, Canavieira LM, Cardoso ÉTC, Silva EO, Lameira J, Nascimento JLM, Eifler-Lima VL, Macchi BM, Sriram D, Bernhardt PV, Silva JRA, Williams CM, Alves CN.

Chem Biol Drug Des. 2017 Nov;90(5):804-810. doi: 10.1111/cbdd.13001. Epub 2017 Jun 12.

PMID:
28390091
10.

Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme from Pseudomonas aeruginosa.

Lima AH, Dos Santos AM, Alves CN, Lameira J.

Chem Biol Drug Des. 2017 Apr;89(4):599-607. doi: 10.1111/cbdd.12882. Epub 2016 Nov 16.

PMID:
27736019
11.

Exploring the origin of the catalytic power and product specificity of SET domain protein methyltransferase.

Lima AH, Alves CN, Prasad R, Lameira J.

Mol Biosyst. 2016 Oct 20;12(10):2980-3. doi: 10.1039/c6mb00414h. Epub 2016 Aug 1.

PMID:
27477893
12.

A Computational Analysis of Indomethacin Derivative as Tubulin Inhibitor: Insights into Development of Chemotherapeutic Agents.

Costa KM, Alves CN, Silva JR, Lameira J.

Comb Chem High Throughput Screen. 2016;19(6):431-6.

PMID:
27141989
13.

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.

Lameira J, Kupchencko I, Warshel A.

J Phys Chem B. 2016 Mar 10;120(9):2155-64. doi: 10.1021/acs.jpcb.5b11966. Epub 2016 Feb 29.

14.

Binding Free Energy Calculations of Nine FDA-approved Protease Inhibitors Against HIV-1 Subtype C I36T↑T Containing 100 Amino Acids Per Monomer.

Lockhat HA, Silva JR, Alves CN, Govender T, Lameira J, Maguire GE, Sayed Y, Kruger HG.

Chem Biol Drug Des. 2016 Apr;87(4):487-98. doi: 10.1111/cbdd.12690. Epub 2016 Jan 29.

PMID:
26613568
15.

A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis.

Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GE, Lameira J, Lamichhane G, Kruger HG, Honarparvar B.

J Biomol Struct Dyn. 2016 Nov;34(11):2399-417. doi: 10.1080/07391102.2015.1117397. Epub 2016 Apr 4.

PMID:
26612108
16.

Simulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems.

Silva JR, Govender T, Maguire GE, Kruger HG, Lameira J, Roitberg AE, Alves CN.

Chem Commun (Camb). 2015 Aug 14;51(63):12560-2. doi: 10.1039/c5cc03202d.

PMID:
26153571
17.

Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study.

Honarparvar B, Pawar SA, Alves CN, Lameira J, Maguire GE, Silva JR, Govender T, Kruger HG.

J Biomed Sci. 2015 Feb 18;22:15. doi: 10.1186/s12929-015-0115-5.

18.

Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2.

Silva JR, Bishai WR, Govender T, Lamichhane G, Maguire GE, Kruger HG, Lameira J, Alves CN.

J Biomol Struct Dyn. 2016;34(2):304-17. doi: 10.1080/07391102.2015.1029000. Epub 2015 Jul 24.

PMID:
25762064
19.

Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development.

Moraes GL, Gomes GC, Monteiro de Sousa PR, Alves CN, Govender T, Kruger HG, Maguire GE, Lamichhane G, Lameira J.

Tuberculosis (Edinb). 2015 Mar;95(2):95-111. doi: 10.1016/j.tube.2015.01.006. Epub 2015 Jan 29. Review.

20.

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.

Lameira J, Bora RP, Chu ZT, Warshel A.

Proteins. 2015 Feb;83(2):318-30. doi: 10.1002/prot.24717. Epub 2015 Jan 7.

21.

Combined kinetic studies and computational analysis on kojic acid analogous as tyrosinase inhibitors.

Lima CR, Silva JR, de Tássia Carvalho Cardoso E, Silva EO, Lameira J, do Nascimento JL, do Socorro Barros Brasil D, Alves CN.

Molecules. 2014 Jul 7;19(7):9591-605. doi: 10.3390/molecules19079591.

22.

Structural analysis of viral infectivity factor of HIV type 1 and its interaction with A3G, EloC and EloB.

da Costa KS, Leal E, dos Santos AM, Lima e Lima AH, Alves CN, Lameira J.

PLoS One. 2014 Feb 26;9(2):e89116. doi: 10.1371/journal.pone.0089116. eCollection 2014.

23.

Quantitative exploration of the molecular origin of the activation of GTPase.

B RP, Plotnikov NV, Lameira J, Warshel A.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20509-14. doi: 10.1073/pnas.1319854110. Epub 2013 Nov 26.

24.

Computational study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi.

Silva Nde F, Lameira J, Alves CN, Martí S.

Phys Chem Chem Phys. 2013 Nov 21;15(43):18863-71. doi: 10.1039/c3cp52692e.

PMID:
24084894
25.

Analysis of the structure of calpain-10 and its interaction with the protease inhibitor SNJ-1715.

da Silva RC, de Alencar NA, Alves CN, Lameira J.

Comput Biol Med. 2013 Oct;43(10):1334-40. doi: 10.1016/j.compbiomed.2013.07.010. Epub 2013 Jul 17.

26.

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach.

Reis M, Alves CN, Lameira J, Tuñón I, Martí S, Moliner V.

Phys Chem Chem Phys. 2013 Mar 21;15(11):3772-85. doi: 10.1039/c3cp43968b.

PMID:
23389436
27.

Protein-ligand interaction study of CpOGA in complex with GlcNAcstatin.

Sousa PR, de Alencar NA, Lima AH, Lameira J, Alves CN.

Chem Biol Drug Des. 2013 Feb;81(2):284-90. doi: 10.1111/cbdd.12078. Epub 2012 Nov 27.

PMID:
23066949
28.

Computational analysis of human OGA structure in complex with PUGNAc and NAG-thiazoline derivatives.

de Alencar NA, Sousa PR, Silva JR, Lameira J, Alves CN, Martí S, Moliner V.

J Chem Inf Model. 2012 Oct 22;52(10):2775-83. doi: 10.1021/ci2006005. Epub 2012 Sep 18.

PMID:
22937904
29.

Molecular modeling of T. rangeli, T. brucei gambiense, and T. evansi sialidases in complex with the DANA inhibitor.

Lima AH, Souza PR, Alencar N, Lameira J, Govender T, Kruger HG, Maguire GE, Alves CN.

Chem Biol Drug Des. 2012 Jul;80(1):114-20. doi: 10.1111/j.1747-0285.2012.01380.x. Epub 2012 Apr 13.

PMID:
22416952
30.

Structure modeling of a metalloendopeptidase from Corynebacterium pseudotuberculosis.

Guimarães LC, Silva NF, Miyoshi A, Schneider MP, Silva A, Azevedo V, Brasil DS, Lameira J, Alves CN.

Comput Biol Med. 2012 May;42(5):538-41. doi: 10.1016/j.compbiomed.2012.01.006. Epub 2012 Feb 18.

PMID:
22342425
31.

Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP from Corynebacterium pseudotuberculosis.

Moraes G, Azevedo V, Costa M, Miyoshi A, Silva A, da Silva V, de Oliveira D, Teixeira MF, Lameira J, Alves CN.

J Mol Model. 2012 Mar;18(3):1219-27. doi: 10.1007/s00894-011-1145-x. Epub 2011 Jun 24.

PMID:
21701810
32.

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.

Lameira J, Alves CN, Tuñón I, Martí S, Moliner V.

J Phys Chem B. 2011 May 26;115(20):6764-75. doi: 10.1021/jp202079e. Epub 2011 May 4.

PMID:
21542586
33.

Computational analysis of aspartic protease plasmepsin II complexed with EH58 inhibitor: a QM/MM MD study.

de Farias Silva N, Lameira J, Alves CN.

J Mol Model. 2011 Oct;17(10):2631-8. doi: 10.1007/s00894-011-0963-1. Epub 2011 Jan 25.

PMID:
21264482
34.

Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of CpNagJ in complex with PUGNAc.

Lameira J, Alves CN, Moliner V, Martí S, Castillo R, Tuñón I.

J Phys Chem B. 2010 May 27;114(20):7029-36. doi: 10.1021/jp9115673.

PMID:
20429600
35.

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline.

Lameira J, Alves CN, Moliner V, Martí S, Kanaan N, Tuñón I.

J Phys Chem B. 2008 Nov 13;112(45):14260-6. doi: 10.1021/jp804626j. Epub 2008 Oct 22. Erratum in: J Phys Chem B. 2010 Feb 11;114(5):2090.

PMID:
18939790
36.

A theoretical study of phenolic compounds with antioxidant properties.

Reis M, Lobato B, Lameira J, Santos AS, Alves CN.

Eur J Med Chem. 2007 Apr;42(4):440-6. Epub 2006 Nov 29.

PMID:
17227686
37.

Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: a density functional theory study.

Lameira J, Medeiros IG, Reis M, Santos AS, Alves CN.

Bioorg Med Chem. 2006 Nov 1;14(21):7105-12. Epub 2006 Aug 4.

PMID:
16890444
38.

A density functional study of flavonoid compounds with anti-HIV activity.

Lameira J, Alves CN, Moliner V, Silla E.

Eur J Med Chem. 2006 May;41(5):616-23. Epub 2006 Mar 13.

PMID:
16530886

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