Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An <i>in Silico</i> Approach

Kayapan Satya Dharshan

doi:doi:10.11648/j.cbb.20180602.12

| Peer-Reviewed

Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach

Kayapan Satya Dharshan

Published in Computational Biology and Bioinformatics (Volume 6, Issue 2)

Received: 1 October 2018 Accepted: 19 November 2018 Published: 18 December 2018

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Background: A cascade of enzymes acting in union is involved in the natural wound healing pharmacology of humans making the process a lengthy one. This in turns necessitates new synthetic molecules effective in accelerating the wound healing process. Objective: The present work deals with synthetic molecules aimed at healing wounds targeting the essential enzymes involved in the wound healing process. Method: A series of in house synthesized dalethyne derivatives have been studied in the present work based on their ability to interact with the requisite proteins using docking methodology and degree of interactions of the molecules with each of the proteins have been determined based on their binding energy values. Subsequently, the inhibitory concentrations of the molecules were also predicted based of docking statistics. The validation of the procedure was performed based on the docking interactions of the native ligand. Results: The dalethyne derivatives showed effective interactions with the amino acid residues present in the active site of some of the essential proteins involved in the wound healing process accounting for the conducive effects of these molecules in the wound healing process. Conclusion: The present work thus provides a meaningful insight as to the structural requirements of the dalethyne derivatives that would facilitate their interaction with the receptors involved in the wound healing process such that the molecules can be efficiently formulated into a pharmaceutical dosage form.

Published in	Computational Biology and Bioinformatics (Volume 6, Issue 2)
DOI	10.11648/j.cbb.20180602.12
Page(s)	36-51
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2018. Published by Science Publishing Group

Keywords

Dalethyne, Docking, In Silico, Wound Healing, Inflammation

References

[1]	S. A. Eming, T. Krieg, and J. M. Davidson (2007) Inflammation in wound repair: molecular and cellular mechanisms. Journal of investigative dermatology 127, 514-525.
[2]	D. A. Enoch, H. A. Ludlam, N. M. Brown (2006) Invasive fungal infections: a review of epidemiology and management options. Journal of medical microbiology 55, 809-818.
[3]	D. J. Leaper, and K. G. Harding, Wounds: biology and management. Oxford: Oxford University Press. 1998.
[4]	G. Topman, N. Shoham, O. Sharabani-Yosef, F. H. Lin, A. Gefen (2013) A new technique for studying directional cell migration in a hydrogel-based three-dimensional matrix for tissue engineering model systems. Micron 51, 9-12.
[5]	D. L. Epstein, L. L. Rowlett, and B. C. Roberts (1999) Acto-myosin drug effects and aqueous outflow function. Investigative Ophthalmology & Visual Science 40, 74–81.
[6]	M. Kulac, C. Aktas, F. Tulubas, R. Uygur, M. Kanter, M. Erboga, M. Ceber, B. Topcu, O. A. Ozen (2013) The effects of topical treatment with curcumin on burn wound healing in rats Journal of Molecular Histology 44, 83-90.
[7]	C. Mohanty, M. Das, and S. K. Sahoo (2012) Sustained wound healing activity of curcumin loaded oleic acid based polymeric bandage in a rat model. Molecular pharmaceutics 9, 2801-2811.
[8]	M. Siavash, S. Shokri, S. Haghighi, M. A. Shahtalebi, Z. Farajzadehgan (2015) The efficacy of topical royal jelly on healing of diabetic foot ulcers: a double-blind placebo-controlled clinical trial. International wound journal 12, 137-142.
[9]	M. Chen, H. Zheng, L. P. Yin, C. G. Xie (2010) Is oral administration of Chinese herbal medicine effective and safe as an adjunctive therapy for managing diabetic foot ulcers? A systematic review and meta-analysis. Journal of Alternative and Complementary Medicine 16, 889-898.
[10]	J. W. Alexander, and D. M. Supp (2014) Role of arginine and omega-3 fatty acids in wound healing and infection. Advances in wound care (New Rochelle). 3, 682–690.
[11]	T. Schultz, (2003) Quantitative Structure–Activity Relationships (QSARs) in Toxicology: A Historical Perspective. Journal of molecular structure: Theochem. 622, 1-22.
[12]	T. Lengauer, and M, Rarey (1996) Computational methods for biomolecular docking. Current Opinion in Structural Biology 6, 402–406.
[13]	A. Singh, A. Mishra, S. Verma, V. Purohit, R. K. Goel, (2014). Regulation of wound strength by Ocimum sanctum: in silico and in vivo evidences. International Journal of Basic & Clinical Pharmacology 3, 179-185.
[14]	M. Incerti, L. Crascì, P. Vicini, E. Aki, I. Yalcin, T. Ertan-Bolelli, V. Cardile, A. C. E. Graziano, A. Panico (2018) Thiazolidinone derivatives as MMP inhibitors in tissue damage: Synthesis, biological evaluation and docking studies. Molecules 23, 415.
[15]	A. Islam, M. S Hafez Kabir, R. Dash, T. B. Emran, M. Z. Uddin, K. Nesa, M. M. Nasir Uddin, M. T. Ahsan (2015). Virtual screening for potential COX-inhibiting constituents from Mimosa pudica. Journal of Applied Pharmaceutical Science 5, 71-75.
[16]	K. S. Dharshan, (2018) Effect of +Dalethyne on Pseudomonas aeruginosa. Ijppr. Human. 12, 258-266.
[17]	Ervina WF, A. D. W. Widodo and Y. P. Dahlan (2017) Pengaruh pemberian +dalethyne terhadap jumlah ekspresi il-1β pada tikus yang diinfeksi P. aeruginosa. Journal of Biosains Pascasarjana 19 (available online only).
[18]	Marvin sketch (version. 6.0), 2013, ChemAxon (http://www.chemaxon.com).
[19]	Protein Data Bank, www.rscb.org.
[20]	Autodock 4.2, AutoDock Vina (http://vina.scripps.edu), 2006.
[21]	PyMOL: The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC
[22]	L. Koivisto, L. Hakkinen and H. Larjava, (2011) Re-epithelialization of wounds. Endodontic Topics, 24: 59–93.
[23]	J. H. Wang, G. Yang, Z. Li, W. Shen (2004) Fibroblast responses to cyclic mechanical stretching depend on cell orientation to the stretching direction. J Biomechanics 37: 573–576.
[24]	S. Guo, and L. A. Di Pietro (2010) Factors affecting wound healing. Journal of dental research 89, 219–229.

Cite This Article

Plain Text BibTeX RIS

APA Style

Kayapan Satya Dharshan. (2018). Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Computational Biology and Bioinformatics, 6(2), 36-51. https://doi.org/10.11648/j.cbb.20180602.12

Copy | Download

ACS Style

Kayapan Satya Dharshan. Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Comput. Biol. Bioinform. 2018, 6(2), 36-51. doi: 10.11648/j.cbb.20180602.12

Copy | Download

AMA Style

Kayapan Satya Dharshan. Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Comput Biol Bioinform. 2018;6(2):36-51. doi: 10.11648/j.cbb.20180602.12

Copy | Download

@article{10.11648/j.cbb.20180602.12,
  author = {Kayapan Satya Dharshan},
  title = {Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach},
  journal = {Computational Biology and Bioinformatics},
  volume = {6},
  number = {2},
  pages = {36-51},
  doi = {10.11648/j.cbb.20180602.12},
  url = {https://doi.org/10.11648/j.cbb.20180602.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20180602.12},
  abstract = {Background: A cascade of enzymes acting in union is involved in the natural wound healing pharmacology of humans making the process a lengthy one. This in turns necessitates new synthetic molecules effective in accelerating the wound healing process. Objective: The present work deals with synthetic molecules aimed at healing wounds targeting the essential enzymes involved in the wound healing process. Method: A series of in house synthesized dalethyne derivatives have been studied in the present work based on their ability to interact with the requisite proteins using docking methodology and degree of interactions of the molecules with each of the proteins have been determined based on their binding energy values. Subsequently, the inhibitory concentrations of the molecules were also predicted based of docking statistics. The validation of the procedure was performed based on the docking interactions of the native ligand. Results: The dalethyne derivatives showed effective interactions with the amino acid residues present in the active site of some of the essential proteins involved in the wound healing process accounting for the conducive effects of these molecules in the wound healing process. Conclusion: The present work thus provides a meaningful insight as to the structural requirements of the dalethyne derivatives that would facilitate their interaction with the receptors involved in the wound healing process such that the molecules can be efficiently formulated into a pharmaceutical dosage form.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach
AU  - Kayapan Satya Dharshan
Y1  - 2018/12/18
PY  - 2018
N1  - https://doi.org/10.11648/j.cbb.20180602.12
DO  - 10.11648/j.cbb.20180602.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 36
EP  - 51
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20180602.12
AB  - Background: A cascade of enzymes acting in union is involved in the natural wound healing pharmacology of humans making the process a lengthy one. This in turns necessitates new synthetic molecules effective in accelerating the wound healing process. Objective: The present work deals with synthetic molecules aimed at healing wounds targeting the essential enzymes involved in the wound healing process. Method: A series of in house synthesized dalethyne derivatives have been studied in the present work based on their ability to interact with the requisite proteins using docking methodology and degree of interactions of the molecules with each of the proteins have been determined based on their binding energy values. Subsequently, the inhibitory concentrations of the molecules were also predicted based of docking statistics. The validation of the procedure was performed based on the docking interactions of the native ligand. Results: The dalethyne derivatives showed effective interactions with the amino acid residues present in the active site of some of the essential proteins involved in the wound healing process accounting for the conducive effects of these molecules in the wound healing process. Conclusion: The present work thus provides a meaningful insight as to the structural requirements of the dalethyne derivatives that would facilitate their interaction with the receptors involved in the wound healing process such that the molecules can be efficiently formulated into a pharmaceutical dosage form.
VL  - 6
IS  - 2
ER  -

Copy | Download

Author Information

Kayapan Satya Dharshan

Department of Wound Care, PT Dermozone Pratama Indonesia, Jakarta, Indonesia

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Kayapan Satya Dharshan. (2018). Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Computational Biology and Bioinformatics, 6(2), 36-51. https://doi.org/10.11648/j.cbb.20180602.12

Copy | Download

ACS Style

Kayapan Satya Dharshan. Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Comput. Biol. Bioinform. 2018, 6(2), 36-51. doi: 10.11648/j.cbb.20180602.12

Copy | Download

AMA Style

Kayapan Satya Dharshan. Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach. Comput Biol Bioinform. 2018;6(2):36-51. doi: 10.11648/j.cbb.20180602.12

Copy | Download

@article{10.11648/j.cbb.20180602.12,
  author = {Kayapan Satya Dharshan},
  title = {Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach},
  journal = {Computational Biology and Bioinformatics},
  volume = {6},
  number = {2},
  pages = {36-51},
  doi = {10.11648/j.cbb.20180602.12},
  url = {https://doi.org/10.11648/j.cbb.20180602.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20180602.12},
  abstract = {Background: A cascade of enzymes acting in union is involved in the natural wound healing pharmacology of humans making the process a lengthy one. This in turns necessitates new synthetic molecules effective in accelerating the wound healing process. Objective: The present work deals with synthetic molecules aimed at healing wounds targeting the essential enzymes involved in the wound healing process. Method: A series of in house synthesized dalethyne derivatives have been studied in the present work based on their ability to interact with the requisite proteins using docking methodology and degree of interactions of the molecules with each of the proteins have been determined based on their binding energy values. Subsequently, the inhibitory concentrations of the molecules were also predicted based of docking statistics. The validation of the procedure was performed based on the docking interactions of the native ligand. Results: The dalethyne derivatives showed effective interactions with the amino acid residues present in the active site of some of the essential proteins involved in the wound healing process accounting for the conducive effects of these molecules in the wound healing process. Conclusion: The present work thus provides a meaningful insight as to the structural requirements of the dalethyne derivatives that would facilitate their interaction with the receptors involved in the wound healing process such that the molecules can be efficiently formulated into a pharmaceutical dosage form.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - Docking Studies for Assessment of Wound Healing Potential of Dalethyne Derivatives: An in Silico Approach
AU  - Kayapan Satya Dharshan
Y1  - 2018/12/18
PY  - 2018
N1  - https://doi.org/10.11648/j.cbb.20180602.12
DO  - 10.11648/j.cbb.20180602.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 36
EP  - 51
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20180602.12
AB  - Background: A cascade of enzymes acting in union is involved in the natural wound healing pharmacology of humans making the process a lengthy one. This in turns necessitates new synthetic molecules effective in accelerating the wound healing process. Objective: The present work deals with synthetic molecules aimed at healing wounds targeting the essential enzymes involved in the wound healing process. Method: A series of in house synthesized dalethyne derivatives have been studied in the present work based on their ability to interact with the requisite proteins using docking methodology and degree of interactions of the molecules with each of the proteins have been determined based on their binding energy values. Subsequently, the inhibitory concentrations of the molecules were also predicted based of docking statistics. The validation of the procedure was performed based on the docking interactions of the native ligand. Results: The dalethyne derivatives showed effective interactions with the amino acid residues present in the active site of some of the essential proteins involved in the wound healing process accounting for the conducive effects of these molecules in the wound healing process. Conclusion: The present work thus provides a meaningful insight as to the structural requirements of the dalethyne derivatives that would facilitate their interaction with the receptors involved in the wound healing process such that the molecules can be efficiently formulated into a pharmaceutical dosage form.
VL  - 6
IS  - 2
ER  -

Copy | Download