Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals

Vikas Jha; Navdeep Kaur; Kabir Thakur; Vrushali Dhamapurkar; Prakruti Kapadia; Shraddha Tiwari; Aparna Sahu; Divya Nikumb; Abhishek Kumar; Shruti Narvekar

doi:doi:10.11648/j.cbb.20221001.16

Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals

Vikas Jha, Navdeep Kaur, Kabir Thakur, Vrushali Dhamapurkar, Prakruti Kapadia, Shraddha Tiwari, Aparna Sahu, Divya Nikumb, Abhishek Kumar, Shruti Narvekar

Published in Computational Biology and Bioinformatics (Volume 10, Issue 1)

Received: 30 May 2022 Accepted: 22 June 2022 Published: 30 June 2022

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Abstract

Background: In tremendously effective antiretroviral therapy for Human Immunodeficiency Virus 1 (HIV1) infections, integrase inhibitors are essential drugs. Resistance resulting from mutations, on the other hand, poses a threat to the medication’s long-term efficacy in HIV-1 infected people. Purpose: The current study utilized in silico techniques, we searched for phytochemicals or compounds that can inhibit the activity of the integrase enzyme. Material & Methods: Compounds were collected from databases, and potential candidates were screened using pharmacokinetics and structure-based virtual screening methodologies. The compounds were docked, and the binding affinity was evaluated to set the cut-off value for selecting compounds. When compared to standard drugs, some compounds had a higher binding affinity. Molecular dynamics simulation was then used to gain insight into the stability of the complexes, revealing two lead compounds, Withaferin and Isatin, indicating that these compounds have potency for drug development. These compounds were further investigated for their toxicity, indicating that Isatin was safe among the two. Conclusion: Thus, the study showcased that Isatin is a suitable drug candidate, and we hope that the findings of this study will be useful in the development of an antiviral drug against integrase enzyme.

Published in	Computational Biology and Bioinformatics (Volume 10, Issue 1)
DOI	10.11648/j.cbb.20221001.16
Page(s)	34-48
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), 2024. Published by Science Publishing Group

Keywords

Human Immunodeficiency Virus 1 (HIV1), Integrase, Molecular Docking, Molecular Dynamic Simulation

References

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APA Style

Vikas Jha, Navdeep Kaur, Kabir Thakur, Vrushali Dhamapurkar, Prakruti Kapadia, et al. (2022). Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Computational Biology and Bioinformatics, 10(1), 34-48. https://doi.org/10.11648/j.cbb.20221001.16

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ACS Style

Vikas Jha; Navdeep Kaur; Kabir Thakur; Vrushali Dhamapurkar; Prakruti Kapadia, et al. Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Comput. Biol. Bioinform. 2022, 10(1), 34-48. doi: 10.11648/j.cbb.20221001.16

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AMA Style

Vikas Jha, Navdeep Kaur, Kabir Thakur, Vrushali Dhamapurkar, Prakruti Kapadia, et al. Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Comput Biol Bioinform. 2022;10(1):34-48. doi: 10.11648/j.cbb.20221001.16

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@article{10.11648/j.cbb.20221001.16,
  author = {Vikas Jha and Navdeep Kaur and Kabir Thakur and Vrushali Dhamapurkar and Prakruti Kapadia and Shraddha Tiwari and Aparna Sahu and Divya Nikumb and Abhishek Kumar and Shruti Narvekar},
  title = {Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals},
  journal = {Computational Biology and Bioinformatics},
  volume = {10},
  number = {1},
  pages = {34-48},
  doi = {10.11648/j.cbb.20221001.16},
  url = {https://doi.org/10.11648/j.cbb.20221001.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20221001.16},
  abstract = {Background: In tremendously effective antiretroviral therapy for Human Immunodeficiency Virus 1 (HIV1) infections, integrase inhibitors are essential drugs. Resistance resulting from mutations, on the other hand, poses a threat to the medication’s long-term efficacy in HIV-1 infected people. Purpose: The current study utilized in silico techniques, we searched for phytochemicals or compounds that can inhibit the activity of the integrase enzyme. Material & Methods: Compounds were collected from databases, and potential candidates were screened using pharmacokinetics and structure-based virtual screening methodologies. The compounds were docked, and the binding affinity was evaluated to set the cut-off value for selecting compounds. When compared to standard drugs, some compounds had a higher binding affinity. Molecular dynamics simulation was then used to gain insight into the stability of the complexes, revealing two lead compounds, Withaferin and Isatin, indicating that these compounds have potency for drug development. These compounds were further investigated for their toxicity, indicating that Isatin was safe among the two. Conclusion: Thus, the study showcased that Isatin is a suitable drug candidate, and we hope that the findings of this study will be useful in the development of an antiviral drug against integrase enzyme.},
 year = {2022}
}

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TY  - JOUR
T1  - Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals
AU  - Vikas Jha
AU  - Navdeep Kaur
AU  - Kabir Thakur
AU  - Vrushali Dhamapurkar
AU  - Prakruti Kapadia
AU  - Shraddha Tiwari
AU  - Aparna Sahu
AU  - Divya Nikumb
AU  - Abhishek Kumar
AU  - Shruti Narvekar
Y1  - 2022/06/30
PY  - 2022
N1  - https://doi.org/10.11648/j.cbb.20221001.16
DO  - 10.11648/j.cbb.20221001.16
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 34
EP  - 48
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20221001.16
AB  - Background: In tremendously effective antiretroviral therapy for Human Immunodeficiency Virus 1 (HIV1) infections, integrase inhibitors are essential drugs. Resistance resulting from mutations, on the other hand, poses a threat to the medication’s long-term efficacy in HIV-1 infected people. Purpose: The current study utilized in silico techniques, we searched for phytochemicals or compounds that can inhibit the activity of the integrase enzyme. Material & Methods: Compounds were collected from databases, and potential candidates were screened using pharmacokinetics and structure-based virtual screening methodologies. The compounds were docked, and the binding affinity was evaluated to set the cut-off value for selecting compounds. When compared to standard drugs, some compounds had a higher binding affinity. Molecular dynamics simulation was then used to gain insight into the stability of the complexes, revealing two lead compounds, Withaferin and Isatin, indicating that these compounds have potency for drug development. These compounds were further investigated for their toxicity, indicating that Isatin was safe among the two. Conclusion: Thus, the study showcased that Isatin is a suitable drug candidate, and we hope that the findings of this study will be useful in the development of an antiviral drug against integrase enzyme.
VL  - 10
IS  - 1
ER  -

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Author Information

Vikas Jha

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Navdeep Kaur

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Kabir Thakur

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Vrushali Dhamapurkar

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Prakruti Kapadia

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Shraddha Tiwari

Department of Biotechnology, B. K. Birla College, Kalyan, India
Aparna Sahu

Department of Biotechnology, B. K. Birla College, Kalyan, India
Divya Nikumb

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Abhishek Kumar

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India
Shruti Narvekar

National Facility for Biopharmaceuticals, Guru Nanak Khalsa College of Arts, Science & Commerce, Mumbai, India

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APA Style

Vikas Jha, Navdeep Kaur, Kabir Thakur, Vrushali Dhamapurkar, Prakruti Kapadia, et al. (2022). Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Computational Biology and Bioinformatics, 10(1), 34-48. https://doi.org/10.11648/j.cbb.20221001.16

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ACS Style

Vikas Jha; Navdeep Kaur; Kabir Thakur; Vrushali Dhamapurkar; Prakruti Kapadia, et al. Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Comput. Biol. Bioinform. 2022, 10(1), 34-48. doi: 10.11648/j.cbb.20221001.16

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AMA Style

Vikas Jha, Navdeep Kaur, Kabir Thakur, Vrushali Dhamapurkar, Prakruti Kapadia, et al. Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals. Comput Biol Bioinform. 2022;10(1):34-48. doi: 10.11648/j.cbb.20221001.16

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@article{10.11648/j.cbb.20221001.16,
  author = {Vikas Jha and Navdeep Kaur and Kabir Thakur and Vrushali Dhamapurkar and Prakruti Kapadia and Shraddha Tiwari and Aparna Sahu and Divya Nikumb and Abhishek Kumar and Shruti Narvekar},
  title = {Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals},
  journal = {Computational Biology and Bioinformatics},
  volume = {10},
  number = {1},
  pages = {34-48},
  doi = {10.11648/j.cbb.20221001.16},
  url = {https://doi.org/10.11648/j.cbb.20221001.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20221001.16},
  abstract = {Background: In tremendously effective antiretroviral therapy for Human Immunodeficiency Virus 1 (HIV1) infections, integrase inhibitors are essential drugs. Resistance resulting from mutations, on the other hand, poses a threat to the medication’s long-term efficacy in HIV-1 infected people. Purpose: The current study utilized in silico techniques, we searched for phytochemicals or compounds that can inhibit the activity of the integrase enzyme. Material & Methods: Compounds were collected from databases, and potential candidates were screened using pharmacokinetics and structure-based virtual screening methodologies. The compounds were docked, and the binding affinity was evaluated to set the cut-off value for selecting compounds. When compared to standard drugs, some compounds had a higher binding affinity. Molecular dynamics simulation was then used to gain insight into the stability of the complexes, revealing two lead compounds, Withaferin and Isatin, indicating that these compounds have potency for drug development. These compounds were further investigated for their toxicity, indicating that Isatin was safe among the two. Conclusion: Thus, the study showcased that Isatin is a suitable drug candidate, and we hope that the findings of this study will be useful in the development of an antiviral drug against integrase enzyme.},
 year = {2022}
}

Copy | Download

TY  - JOUR
T1  - Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of Integrase from Human Immunodeficiency Virus 1 (HIV-1) Using Phytochemicals
AU  - Vikas Jha
AU  - Navdeep Kaur
AU  - Kabir Thakur
AU  - Vrushali Dhamapurkar
AU  - Prakruti Kapadia
AU  - Shraddha Tiwari
AU  - Aparna Sahu
AU  - Divya Nikumb
AU  - Abhishek Kumar
AU  - Shruti Narvekar
Y1  - 2022/06/30
PY  - 2022
N1  - https://doi.org/10.11648/j.cbb.20221001.16
DO  - 10.11648/j.cbb.20221001.16
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 34
EP  - 48
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20221001.16
AB  - Background: In tremendously effective antiretroviral therapy for Human Immunodeficiency Virus 1 (HIV1) infections, integrase inhibitors are essential drugs. Resistance resulting from mutations, on the other hand, poses a threat to the medication’s long-term efficacy in HIV-1 infected people. Purpose: The current study utilized in silico techniques, we searched for phytochemicals or compounds that can inhibit the activity of the integrase enzyme. Material & Methods: Compounds were collected from databases, and potential candidates were screened using pharmacokinetics and structure-based virtual screening methodologies. The compounds were docked, and the binding affinity was evaluated to set the cut-off value for selecting compounds. When compared to standard drugs, some compounds had a higher binding affinity. Molecular dynamics simulation was then used to gain insight into the stability of the complexes, revealing two lead compounds, Withaferin and Isatin, indicating that these compounds have potency for drug development. These compounds were further investigated for their toxicity, indicating that Isatin was safe among the two. Conclusion: Thus, the study showcased that Isatin is a suitable drug candidate, and we hope that the findings of this study will be useful in the development of an antiviral drug against integrase enzyme.
VL  - 10
IS  - 1
ER  -

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