Computer-Based Tools for Structural Characterizations and Activity Specifications of Natural Products: A Quick Review

Authors

  • Hasan Zandi Department of Chemistry, Faculty of Science, University of Qom, Qom, Iran
  • Kun Harismah Department of Chemical Engineering, Faculty of Engineering, Universitas Muhammadiyah Surakarta, Surakarta, Indonesia https://orcid.org/0000-0002-8231-8164

DOI:

https://doi.org/10.22034/labinsilico21021050

Keywords:

Natural product, Computer, In silico, Molecular modeling, Computational analysis

Abstract

Natural products have been always known for their benefits for supplying food and drug for human kind survival for whole history. Using original forms of such compounds or their essential substances could provide several types of applications. Besides highlighted benefits, several limitations prevent such substances to work properly for people of all around the world. Therefore, carful examining their structural characterizations and activity specifications could help to provide specified functions or to propose new related derivatives. Computer-based tools are among useful tools for achieving such purposes, in which the model systems could be investigated at the lowest molecular and atomic scales. Such works provide in silico media for investigating various features of structures and their related functions. As a consequence, further developments of natural products for specified purposes could be led by the means of computer-based tools.

References

Chemat F, Vian MA, Fabiano-Tixier AS, Nutrizio M, Jambrak AR, Munekata PE, Lorenzo JM, Barba FJ, Binello A, Cravotto G. A review of sustainable and intensified techniques for extraction of food and natural products. Green Chemistry. 2020;22:2325-2353.

Isman MB. Commercial development of plant essential oils and their constituents as active ingredients in bioinsecticides. Phytochemistry Reviews. 2020;19:235-241.

Raheem MA, Jiangang H, Yin D, Xue M, ur Rehman K, Rahim MA, Gu Y, Fu D, Song X, Tu J, Khan IM. Response of lymphatic tissues to natural feed additives; curcumin (Curcuma longa) and black cumin seeds (Nigella sativa) in broilers against Pasteurella multocida. Poultry Science. 2021:in press.

Zahedipour F, Hosseini SA, Sathyapalan T, Majeed M, Jamialahmadi T, Al?Rasadi K, Banach M, Sahebkar A. Potential effects of curcumin in the treatment of COVID?19 infection. Phytotherapy Research. 2020;34:2911-2920.

Mansouri K, Rasoulpoor S, Daneshkhah A, Abolfathi S, Salari N, Mohammadi M, Rasoulpoor S, Shabani S. Clinical effects of curcumin in enhancing cancer therapy: a systematic review. BMC Cancer. 2020;20:791.

Harismah K, Mirzaei M, Fuadi AM. Stevia rebaudiana in food and beverage applications and its potential antioxidant and antidiabetic: mini review. Advanced Science Letters. 2018;24:9133-9137.

Pertiwi WS, Manikam AS, Hidayanto A, Harismah K. Efektivitas antibakteri ekstrak daun stevia (Stevia rebaudiana) dan minyak cengkeh sebagai obat kumur herbal alami menggunakan metode infundasi. URECOL. 2017:177-182.

Harismah K. Pembuatan yogurt susu sapi dengan pemanis stevia sebagai sumber kalsium untuk mencegah osteoporosis. Jurnal Teknologi Bahan Alam. 2017;1:29-34.

Handayani Z, Prasetyo JY, Harismah K. Uji organoleptik dan kadar glukosa yoghurt kulit semangka dengan substitusi pemanis sukrosa dan ekstrak daun stevia (Stevia rebaudiana). URECOL. 2017:147-156.

Chen Y, Garcia de Lomana M, Friedrich NO, Kirchmair J. Characterization of the chemical space of known and readily obtainable natural products. Journal of Chemical Information and Modeling. 2018;58:1518-1532.

Olmedo DA, González-Medina M, Gupta MP, Medina-Franco JL. Cheminformatic characterization of natural products from Panama. Molecular Diversity. 2017;21:779-789.

Deans BJ, Just J, Smith JA, Bissember AC. Development and applications of water?based extraction methods in natural products isolation chemistry. Asian Journal of Organic Chemistry. 2020;9:1144-1153.

Gonçalves GA, Spillere AR, das Neves GM, Kagami LP, von Poser GL, Canto RF, Eifler-Lima VL. Natural and synthetic coumarins as antileishmanial agents: a review. European Journal of Medicinal Chemistry. 2020;203:112514.

Gaston TE, Mendrick DL, Paine MF, Roe AL, Yeung CK. “Natural” is not synonymous with “safe”: toxicity of natural products alone and in combination with pharmaceutical agents. Regulatory Toxicology and Pharmacology. 2020;113:104642.

Santos VS, Pereira BB. Properties, toxicity and current applications of the biolarvicide spinosad. Journal of Toxicology and Environmental Health B. 2020;23:13-26.

Cheng Z, Li L, Liu J. Natural resource abundance, resource industry dependence and economic green growth in China. Resources Policy. 2020;68:101734.

Loeschcke A, Thies S. Engineering of natural product biosynthesis in Pseudomonas putida. Current Opinion in Biotechnology. 2020;65:213-224.

Mirzaei M. Science and engineering in silico. Advanced Journal of Science and Engineering. 2020;1:1-2.

Mirzaei M. Lab-in-Silico: an international journal. Lab-in-Silico. 2020;1:1-2.

Mirzaei M. Making sense the ideas in silico. Lab-in-Silico. 2020 Dec 30;1(2):31-2.

Mirzaei M. Lab-in-Silico insights. Advanced Journal of Chemistry B. 2020;2:1-2.

Soleimanimehr H, Mirzaei M. An introduction to Lab-in-Silico. Lab-in-Silico. 2021;2:1-2.

Farahbakhsh Z, Zamani MR, Rafienia M, Gülseren O, Mirzaei M. In silico activity of AS1411 aptamer against nucleolin of cancer cells. Iranian Journal of Blood and Cancer. 2020;12:95-100.

Lim J, Ryu S, Kim JW, Kim WY. Molecular generative model based on conditional variational autoencoder for de novo molecular design. Journal of Cheminformatics. 2018;10:1-9.

Moumbock AF, Li J, Mishra P, Gao M, Günther S. Current computational methods for predicting protein interactions of natural products. Computational and Structural Biotechnology Journal. 2019;17:1367-1376.

Wang L, Dash S, Ng CY, Maranas CD. A review of computational tools for design and reconstruction of metabolic pathways. Synthetic and Systems Biotechnology. 2017;2:243-252.

Mirzaei M, Hadipour NL. An investigation of hydrogen-bonding effects on the nitrogen and hydrogen electric field gradient and chemical shielding tensors in the 9-methyladenine real crystalline structure: a density functional theory study. The Journal of Physical Chemistry A. 2006;110:4833-4838.

Li R, Wijma HJ, Song L, Cui Y, Otzen M, Du J, Li T, Niu D, Chen Y, Feng J, Han J. Computational redesign of enzymes for regio-and enantioselective hydroamination. Nature Chemical Biology. 2018;14:664-670.

Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, De Los Santos EL, Yeong M, Cruz-Morales P, Abubucker S, Roeters A. A computational framework to explore large-scale biosynthetic diversity. Nature Chemical Biology. 2020;16:60-68.

Soleimani M, Mirzaei M. In silico pharmacy: from computations to clinics. Journal of Pharmaceutical Care. 2017:5:1.

Singh H, Singh JV, Bhagat K, Gulati HK, Sanduja M, Kumar N, Kinarivala N, Sharma S. Rational approaches, design strategies, structure activity relationship and mechanistic insights for therapeutic coumarin hybrids. Bioorganic & Medicinal Chemistry. 2019;27:3477-3510.

Itoh H, Inoue M. Comprehensive structure–activity relationship studies of macrocyclic natural products enabled by their total syntheses. Chemical Reviews. 2019;119:10002-10031.

Gilani AG, Taghvaei V, Rufchahi EM, Mirzaei M. Tautomerism, solvatochromism, preferential solvation, and density functional study of some heteroarylazo dyes. Journal of Molecular Liquids. 2019;273:392-407.

Grimme S, Schreiner PR. Computational chemistry: the fate of current methods and future challenges. Angewandte Chemie. 2018;57:4170-4176.

Verma P, Truhlar DG. Status and challenges of density functional theory. Trends in Chemistry. 2020;2:302-318.

Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Advanced Journal of Science and Engineering. 2020;1:62-66.

Nouri A, Mirzaei M. DFT calculations of B-11 and N-15 NMR parameters in BN nanocone. Journal of Molecular Structure: THEOCHEM. 2009;913:207-209.

Alexeev Y, P Mazanetz M, Ichihara O, G Fedorov D. GAMESS as a free quantum-mechanical platform for drug research. Current Topics in Medicinal Chemistry. 2012;12:2013-2033.

Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 09, Revision A.01, Gaussian. Inc., Wallingford CT. 2009.

Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. The Journal of Chemical Physics. 2020;152:224108.

Zhurko GA, Zhurko DA. ChemCraft: Tool for treatment of chemical data. Lite Version Build. 2005;8:2005.

Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics. 2012;4:1-7.

GaussView, Version 6, Dennington, Roy; Keith, Todd A.; Millam, John M. Semichem Inc., KS. 2016.

Pence HE, Williams A. ChemSpider: an online chemical information resource. Journal of Chemical Education. 2010;87:1123-1124.

Mokhtari A, Harismah K, Mirzaei M. Covalent addition of chitosan to graphene sheets: density functional theory explorations of quadrupole coupling constants. Superlattices and Microstructures. 2015;88:56-61.

Yousefvand H, Mirzaei M, Tabbakhian M. Investigating chitosan-curcumin nanorings for containing fluorouracil. Turkish Computational and Theoretical Chemistry. 2017;1:6-12.

Mirzaei M. Drug discovery: a non-expiring process. Advanced Journal of Chemistry B. 2020;2:46-47.

Guo Z. The modification of natural products for medical use. Acta Pharmaceutica Sinica B. 2017;7:119-136.

Pinzi L, Rastelli G. Molecular docking: Shifting paradigms in drug discovery. International Journal of Molecular Sciences. 2019;20:4331.

Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Di Costanzo L, et al. RCSB protein data bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Research. 2019;47:464-474.

Huey R, Morris GM, Forli S. Using AutoDock 4 and AutoDock vina with AutoDockTools: a tutorial. The Scripps Research Institute Molecular Graphics Laboratory. 2012;10550:92037.

Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Research. 2011;39:270-277.

Lill MA, Danielson ML. Computer-aided drug design platform using PyMOL. Journal of computer-aided molecular design. 2011 Jan;25(1):13-9.

BIOVIA, Dassault Systèmes, Discovery Studio, San Diego: Dassault Systèmes. 2016.

Nazemi H, Mirzaei M, Jafari E. Antidepressant activity of curcumin by monoamine oxidase-A inhibition. Advanced Journal of Chemistry B. 2019;1:3-9.

Mirzaei M, Harismah K, Soleimani M, Mousavi S. Inhibitory effects of curcumin on aldose reductase and cyclooxygenase-2 enzymes. Journal of Biomolecular Structure and Dynamics. 2021:in press.

Harismah K, Mirzaei M. Steviol and iso-steviol vs. cyclooxygenase enzymes: in silico approach. Lab-in-Silico. 2020;1:11-15.

Harismah K, Mirzaei M. In silico interactions of steviol with monoamine oxidase enzymes. Lab-in-Silico. 2020;1:3-6.

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Published

2021-03-10

How to Cite

Zandi, H., & Harismah, K. (2021). Computer-Based Tools for Structural Characterizations and Activity Specifications of Natural Products: A Quick Review. Lab-in-Silico, 2(1), 50–54. https://doi.org/10.22034/labinsilico21021050

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Section

Review Article