Conceptual DFT-Based Computational Peptidology of Marine Natural Compounds: Discodermins A-H

被引:34
|
作者
Flores-Holguin, Norma [1 ]
Frau, Juan [2 ]
Glossman-Mitnik, Daniel [1 ]
机构
[1] Ctr Invest Mat Avanzados, Dept Medio Ambiente & Energia, Lab Virtual NANOCOSMOS, Chihuahua 31136, Chih, Mexico
[2] Univ Illes Balears, Dept Quim, E-07122 Palma De Malllorca, Spain
来源
MOLECULES | 2020年 / 25卷 / 18期
关键词
Discodermins A-H; Chemical Reactivity Theory; Conceptual DFT; Global and Local Reactivity Descriptors; pKa; Bioavailability; Bioactivity scores; ADME; MOLECULAR-FORCE FIELD; DUAL DESCRIPTOR; DENSITY FUNCTIONALS; LOCAL REACTIVITY; BASIS-SETS; EXCITATIONS; ENERGIES; PREDICT; INDEX;
D O I
10.3390/molecules25184158
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A-H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kinds of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity, some parameters of usefulness for future QSAR studies, their predicted biological targets, and the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A-H pharmacokinetics are also reported.
引用
收藏
页数:20
相关论文
共 50 条
  • [21] DFT-based microkinetic modeling of ethanol dehydration in H-ZSM-5
    Alexopoulos, Konstantinos
    John, Mathew
    Van der Borght, Kristof
    Galvita, Vladimir
    Reyniers, Marie-Francoise
    Marin, Guy B.
    JOURNAL OF CATALYSIS, 2016, 339 : 173 - 185
  • [22] Excited state intramolecular proton transfer in 3-hydroxychromone: a DFT-based computational study
    Ash, Sankarlal
    De, Sankar Prasad
    Beg, Hasibul
    Misra, Ajay
    MOLECULAR SIMULATION, 2011, 37 (11) : 914 - 922
  • [23] Synthesis, Computational Pharmacokinetics Report, Conceptual DFT-Based Calculations and Anti-Acetylcholinesterase Activity of Hydroxyapatite Nanoparticles Derived From Acorus Calamus Plant Extract
    Pradeep, Sushma
    Jain, Anisha S.
    Dharmashekara, Chandan
    Prasad, Shashanka K.
    Akshatha, Nagaraju
    Pruthvish, R.
    Amachawadi, Raghavendra G.
    Srinivasa, Chandrashekar
    Syed, Asad
    Elgorban, Abdallah M.
    Al Kheraif, Abdulaziz A.
    Ortega-Castro, Joaquin
    Frau, Juan
    Flores-Holguin, Norma
    Shivamallu, Chandan
    Kollur, Shiva Prasad
    Glossman-Mitnik, Daniel
    FRONTIERS IN CHEMISTRY, 2021, 9
  • [24] Investigating the (Poly)Radicaloid Nature of Real-World Organic Compounds with DFT-Based Methods
    Salvitti, Giovanna
    Negri, Fabrizia
    Perez-Jimenez, Angel J.
    San-Fabian, Emilio
    Casanova, David
    Sancho-Garcia, Juan Carlos
    JOURNAL OF PHYSICAL CHEMISTRY A, 2020, 124 (18): : 3590 - 3600
  • [25] Lignin Modification Supported by DFT-Based Theoretical Study as a Way to Produce Competitive Natural Antioxidants
    Lauberte, Liga
    Fabre, Gabin
    Ponomarenko, Jevgenija
    Dizhbite, Tatiana
    Evtuguin, Dmitry, V
    Telysheva, Galina
    Trouillas, Patrick
    MOLECULES, 2019, 24 (09):
  • [26] DFT-based computational investigations of the structural, electronic, elastic, and magnetic properties of ternary Half-Heusler TiVX (X = Ge, Si, Pb, Sn) compounds
    Husain, Mudasser
    Rahman, Nasir
    Sfina, Nourreddine
    Zaman, Tahir
    Al-Shaalan, Nora Hamad
    Alharthi, Sarah
    Alharthy, Saif A.
    Amin, Mohammed A.
    Khan, Rajwali
    Sohail, Mohammad
    Ramli, Muhammad M.
    Reshak, Ali H.
    CHINESE JOURNAL OF PHYSICS, 2024, 89 : 1819 - 1826
  • [27] Toxicity Prediction of Organoph Osphorus Chemical Reactivity Compounds Based on Conceptual DFT
    Ding Xiaoqin
    Ding Junjie
    Li Dayu
    Pan Li
    Pei Chengxin
    ACTA PHYSICO-CHIMICA SINICA, 2018, 34 (03) : 314 - 322
  • [28] Reconciling the Experimental and Computational Hydrogen Evolution Activities of Pt(111) through DFT-Based Constrained MD Simulations
    Kronberg, Rasmus
    Laasonen, Kari
    ACS CATALYSIS, 2021, 11 (13) : 8062 - 8078
  • [29] A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene
    Jaraiz, Martin
    Enriquez, Lourdes
    Pinacho, Ruth
    Rubio, Jose E.
    Lesarri, Alberto
    Lopez-Perez, Jose L.
    JOURNAL OF ORGANIC CHEMISTRY, 2017, 82 (07): : 3760 - 3766
  • [30] A CDFT-Based Computational Peptidology (CDFT-CP) Study of the Chemical Reactivity and Bioactivity of the Marine-Derived Alternaramide Cyclopentadepsipeptide
    Flores-Holguin, Norma
    Frau, Juan
    Glossman-Mitnik, Daniel
    JOURNAL OF CHEMISTRY, 2021, 2021