In search of AKT kinase inhibitors as anticancer agents: structure-based design, docking, and molecular dynamics studies of 2,4,6-trisubstituted pyridines.

Abstract:

:The AKT isoforms are a group of key kinases that play a critical role in tumorigenesis. These enzymes are overexpressed in different types of cancers, such as breast, colon, prostate, ovarian, and lung. Because of its relevance the AKT isoforms are attractive targets for the design of anticancer molecules. However, it has been found that AKT1 and AKT3 isoforms have a main role in tumor progression and metastasis; thus, the identification of AKT isoforms specific inhibitors seems to be a challenge. Previously, we identified an ATP binding pocket pan-AKT inhibitor, this compound is a 2,4,6-trisubstituted pyridine (compound 11), which represents a new interesting scaffold for the developing of AKT inhibitors. Starting from the 2,4,6-trisubstituted pyridine scaffold, and guided by structure-based design technique, 42 new inhibitors were designed and further evaluated in the three AKT isoforms by multiple docking approach and molecular dynamics. Results showed that seven compounds presented binding selectivity for AKT1 and AKT3, better than for AKT2. The binding affinities of these seven compounds on AKT1 and AKT3 isoforms were mainly determined by hydrophobic contributions between the aromatic portion at position 4 of the pyridine ring with residues Phe236/234, Phe237/235, Phe438/435, and Phe442/439 in the ATP binding pocket. Results presented in this work provide an addition knowledge leading to promising selective AKT inhibitors.

journal_name

J Biomol Struct Dyn

authors

Trejo-Soto PJ,Hernández-Campos A,Romo-Mancillas A,Medina-Franco JL,Castillo R

doi

10.1080/07391102.2017.1285724

subject

Has Abstract

pub_date

2018-02-01 00:00:00

pages

423-442

issue

2

eissn

0739-1102

issn

1538-0254

journal_volume

36

pub_type

杂志文章
  • Long, chiral polypeptide 3(10)-helices at atomic resolution.

    abstract::The crystal-state preferred conformation of the terminally blocked hepta- and octapeptides with the general formula -(Aib)n L-Leu-(Aib)2- (n = 4 and 5, respectively), determined by X-ray diffraction, was found to be a right-handed 3(10)-helix stabilized by five and six consecutive intramolecular NH...O = C H-bonds of ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1988.10506428

    authors: Bavoso A,Benedetti E,Di Blasio B,Pavone V,Pedone C,Toniolo C,Bonora GM,Formaggio F,Crisman M

    更新日期:1988-02-01 00:00:00

  • Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing study.

    abstract::The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The virulent nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an in silico based drug repurposing approach to id...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1814870

    authors: Khan RJ,Jha RK,Singh E,Jain M,Amera GM,Singh RP,Muthukumaran J,Singh AK

    更新日期:2020-09-04 00:00:00

  • Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities, in poly(deoxythymidylic acid)-poly-L-lysine complexes.

    abstract::Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10508414

    authors: Bobst AM,Kao SC,Bobst EV,Pauly GT

    更新日期:1985-10-01 00:00:00

  • Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition.

    abstract::With the explosive growth of protein sequences entering into protein data banks in the post-genomic era, it is highly demanded to develop automated methods for rapidly and effectively identifying the protein-protein binding sites (PPBSs) based on the sequence information alone. To address this problem, we proposed a p...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1095116

    authors: Jia J,Liu Z,Xiao X,Liu B,Chou KC

    更新日期:2016-09-01 00:00:00

  • Urea-induced denaturation of human calcium/calmodulin-dependent protein kinase IV: a combined spectroscopic and MD simulation studies.

    abstract::Calcium/calmodulin-dependent protein kinase IV (CaMKIV) is a multifunctional enzyme which belongs to the Ser/Thr kinase family. CaMKIV plays important role in varieties of biological processes such as gene expression regulation, memory consolidation, bone growth, T-cell maturation, sperm motility, regulation of microt...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1150203

    authors: Naz H,Shahbaaz M,Haque MA,Bisetty K,Islam A,Ahmad F,Hassan MI

    更新日期:2017-02-01 00:00:00

  • Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2019.1591306

    authors: Kargatov AM,Efimov AV

    更新日期:2020-03-01 00:00:00

  • A genetic algorithm with conformational memories for structure prediction of polypeptides.

    abstract::We have developed an iterative hybrid algorithm (HA) to predict the 3D structure of peptides starting from their amino acid sequence. The HA is made of a modified genetic algorithm (GA) coupled to a local optimizer. Each HA iteration is carried out in two phases. In the first phase several GA runs are performed upon t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2003.10506906

    authors: Garduño-Juárez R,Morales LB

    更新日期:2003-08-01 00:00:00

  • Cooperative hydrogen bonds and mobility of the non-aromatic ring as selectivity determinants for human acetylcholinesterase to similar anti-Alzheimer's galantaminics: a computational study.

    abstract::Galantamine (Gnt) is a natural alkaloid inhibitor of acetylcholinesterase and is presently one of the most used drugs in the treatment against Alzheimer's disease during both the initial and intermediate stages. Among several natural Gnt derivatives, sanguinine (Sng) and lycoramine (Lyc) attract attention because of t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1470036

    authors: Rocha REO,Lima LHF

    更新日期:2019-04-01 00:00:00

  • Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell.

    abstract::Minidumbbell (MDB) is a newly found non-B DNA structure formed by short single-strand sequences. Up to now, three MDBs have been reported to form at neutral pH by sequences containing two repeats of TTTA, CCTG and CTTG. Among them, the thermodynamically less stable TTTA and CCTG MDBs have been proposed to be the struc...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1621211

    authors: Guo P,Lam SL

    更新日期:2020-04-01 00:00:00

  • Human microtubule affinity-regulating kinase 4 is stable at extremes of pH.

    abstract::MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-ter...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1074942

    authors: Naz F,Singh P,Islam A,Ahmad F,Imtaiyaz Hassan M

    更新日期:2016-06-01 00:00:00

  • Probing the dynamics between the substrate and the product towards glucose tolerance of Halothermothrix orenii β-glucosidase.

    abstract::Most β-Glucosidase (B8CYA8) are prone to inhibition by glucose. Experimentally observed specific activity of B8CYA8 on 20 mM, 50 mM, and 100 mM p-nitrophenyl-β-D-glucopyranoside (pNPGlc) substrate concentrations show surprise dependence on the presence of 0-3 M glucose at 335 K. We found that at high substrate concent...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1796789

    authors: Konar S,Sinha SK,Datta S,Ghorai PK

    更新日期:2020-07-28 00:00:00

  • Structural characterization of vivapain-2 and vivapain-3, cysteine proteases from Plasmodium vivax: comparative protein modeling and docking studies.

    abstract::Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506968

    authors: Desai PV,Avery MA

    更新日期:2004-06-01 00:00:00

  • Insight of druggable cannabinoids against estrogen receptor β in breast cancer.

    abstract::Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1737233

    authors: Bhattacharjee A,Hossain MU,Chowdhury ZM,Rahman SMA,Bhuyan ZA,Salimullah M,Keya CA

    更新日期:2020-03-11 00:00:00

  • The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study.

    abstract::The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1682048

    authors: Santhiya P,Christian Bharathi A,Syed Ibrahim B

    更新日期:2020-09-01 00:00:00

  • Reversible crystal transition of guanosine between the dihydrate and anhydrous states coupled with adsorption-desorption process.

    abstract::Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508028

    authors: Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

    更新日期:1994-02-01 00:00:00

  • Modeling of Neuropeptide Receptors Y1, Y4, Y5, and Docking Studies with Neuropeptide Antagonist Analogues: Implications for Selectivity.

    abstract::Abstract Neuropeptide Y (NPY), receptors belong to the G-protein coupled receptor superfamily. NPY mediates several physiological responses, such as blood pressure, food intake, sedation. These actions of NPY are mediated by six receptor subtypes denoted as Y(1)-Y(5) and y(6). Modeling of receptor subtypes and bindi...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506987

    authors: Jois SD,Nagarajarao LM,Prabhakaran M,Balasubramaniam A

    更新日期:2004-08-01 00:00:00

  • A full-automatic sequence design algorithm for branched DNA structures.

    abstract::Production of various structures by self-assembling single stranded DNA molecules is a widely used technology in the filed of DNA nanotechnology. Base sequences of single strands do predict the shape of the resulting nanostructure. Therefore, sequence design is crucial for the successful structure fabrication. This pa...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507193

    authors: Seiffert J,Huhle A

    更新日期:2008-04-01 00:00:00

  • All-atom molecular dynamics comparison of disease-associated zinc fingers.

    abstract::An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1363662

    authors: Godwin RC,Gmeiner WH,Salsbury FR Jr

    更新日期:2018-08-01 00:00:00

  • The effects of pollen, propolis, and caffeic acid phenethyl ester on tyrosine hydroxylase activity and total RNA levels in hypertensive rats caused by nitric oxide synthase inhibition: experimental, docking and molecular dynamic studies.

    abstract::The objective of the present study was to evaluate the effects of propolis, pollen, and caffeic acid phenethyl ester (CAPE) on tyrosine hydroxylase (TH) activity and total RNA levels of Nω-nitro-L-arginine methyl ester (L-NAME) inhibition of nitric oxide synthase in the heart, adrenal medulla, and hypothalamus of hype...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1288660

    authors: Ekhteiari Salmas R,Durdagi S,Gulhan MF,Duruyurek M,Abdullah HI,Selamoglu Z

    更新日期:2018-02-01 00:00:00

  • The formation of parallel RNA-RNA duplexes in vitro.

    abstract::Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1995.10508860

    authors: Tchurikov NA,Ponomarenko NA,Golova YB,Chernov BK

    更新日期:1995-12-01 00:00:00

  • Theoretical Design, Chemical Synthesis and Footprinting Analysis of a Novel Peptide Derivative of the Intercalator 7-H Pyridocarbazole Targeted Towards the Major Groove of DNA.

    abstract::Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508090

    authors: Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

    更新日期:1994-08-01 00:00:00

  • Handedness of structural units depends on their mutual arrangement in protein structure.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2019.1580220

    authors: Efimov AV

    更新日期:2020-02-01 00:00:00

  • DNA bending and sugar switching.

    abstract::Abstract Using high frequency antiphase NMR spectroscopy and computer simulations of the antiphase spectra, we studied the equlibria in the sugar conformations in the DNA duplex 11-mer containing the AAA tract surrounded by cytosines. We demonstrate that at the 3'-end of the A-tract, the sugar switches from the comm...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506637

    authors: Kamath S,Sarma MH,Zhurkin VB,Turner CJ,Sarma RH

    更新日期:2000-01-01 00:00:00

  • Dynamic instability responses of the substructure living biological cells in the cytoplasm environment using stress-strain size-dependent theory.

    abstract::Over the last few years, some novel researches in the field of medical science made a tendency to have a therapy without any complications or side-effects of the disease with the aid of prognosis about the behaviors of the substructure living biological cell. Regarding this issue, nonlinear frequency characteristics o...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1751297

    authors: Najaafi N,Jamali M,Habibi M,Sadeghi S,Jung DW,Nabipour N

    更新日期:2020-04-17 00:00:00

  • A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions.

    abstract::The coexistence of both A form and B form tracts and formation of an A-B junction in the oligomer d(GGGGGTTTTT).d(AAAAACCCCC) in saturated sodium chloride solution have been detected by Raman spectroscopy. The entire duplex adopts the familiar B-form conformation in aqueous solution at low salt concentrations (0.1M Na...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1989.10506543

    authors: Wang Y,Thomas GA,Peticolas WL

    更新日期:1989-06-01 00:00:00

  • Curcumin-silica nanocomplex preparation, hemoglobin and DNA interaction and photocytotoxicity against melanoma cancer cells.

    abstract::Melanoma is a malignant cancer of the skin associated with a high mortality. Early medical diagnosis and surgical intervention are essential for the treatment of melanoma. The use of plant-based compounds is an important strategy for the prevention and treatment of different types of cancers. Curcumin is a promising n...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1802342

    authors: Ghazaeian M,Khorsandi K,Hosseinzadeh R,Naderi A,Abrahamse H

    更新日期:2020-08-07 00:00:00

  • TIT for TAT: the properties of inosine and adenosine in TATA box DNA.

    abstract::The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1999.10508293

    authors: Pastor N,MacKerell AD Jr,Weinstein H

    更新日期:1999-02-01 00:00:00

  • Fluorescence studies on the coat protein of alfalfa mosaic virus.

    abstract::The intrinsic luminescence of different forms of the alfalfa mosaic virus (AMV) strain 425 coat protein has been studied, both statically and time resolved. It was found that the emission of the protein (Mr 24,250), which contains two tryptophans at positions 54 and 190 and four tyrosines, is completely dominated by t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1986.10508464

    authors: Kan JH,Wijnaendts van Resandt RW,Dekkers HP

    更新日期:1986-02-01 00:00:00

  • Denaturation of HIV-1 protease (PR) monomer by acetic acid: mechanistic and trajectory insights from molecular dynamics simulations and NMR.

    abstract::Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/073911012010525025

    authors: Borkar A,Rout MK,Hosur RV

    更新日期:2012-01-01 00:00:00

  • Monte-Carlo simulation of DNA duplex hydration. B and B' conformations of poly(dA).poly(dT) have different hydration shells.

    abstract::Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1988.10506508

    authors: Poltev VI,Teplukhin AV,Chuprina VP

    更新日期:1988-12-01 00:00:00