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Article

Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease

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Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki 225003, Uttar Pradesh, India
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Department of Biotechnology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow 226021, Uttar Pradesh, India
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Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2240, Saudi Arabia
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Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
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Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
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School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201310, Uttar Pradesh, India
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Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, Uttarakhand, India
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Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, Punjab, India
*
Authors to whom correspondence should be addressed.
Academic Editor: Claudio Torres
Brain Sci. 2022, 12(6), 770; https://doi.org/10.3390/brainsci12060770
Received: 15 February 2022 / Revised: 5 May 2022 / Accepted: 31 May 2022 / Published: 12 June 2022
Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structure prediction of CALHM1 was done through CFSSP, GOR4, and SOPMA methods. The structure was identified through LOMETS, MUSTER, and MODELLER and finally, the structures were validated through Rampage. Bauhinia variegata plant was used to check the interaction of alkaloids and flavonoids against CALHM1. The protein and protein–ligand complex were also validated through molecular dynamics simulations studies. The model generated through MODELLER software with 6VAM A was used because this model predicted the best results in the Ramachandran plot. Further molecular docking was performed, quercetin was found to be the most appropriate candidate for the protein molecule with the minimum binding energy of −12.45 kcal/mol and their ADME properties were analysed through Molsoft and Molinspiration. Molecular dynamics simulations showed that CALHM1 and CALHM1–quercetin complex became stable at 2500 ps. It may be seen through the study that quercetin may act as a good inhibitor for treatment. With the help of an in silico study, it was easier to analyse the 3D structure of the protein, which may be scrutinized for the best-predicted model. Quercetin may work as a good inhibitor for treating Alzheimer’s disease, according to in silico research using molecular docking and molecular dynamics simulations, and future in vitro and in vivo analysis may confirm its effectiveness. View Full-Text
Keywords: homology modelling; LOMETS; MUSTER; iGEMDOCK; AutoDock vina homology modelling; LOMETS; MUSTER; iGEMDOCK; AutoDock vina
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MDPI and ACS Style

Khare, N.; Maheshwari, S.K.; Rizvi, S.M.D.; Albadrani, H.M.; Alsagaby, S.A.; Alturaiki, W.; Iqbal, D.; Zia, Q.; Villa, C.; Jha, S.K.; Jha, N.K.; Jha, A.K. Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease. Brain Sci. 2022, 12, 770. https://doi.org/10.3390/brainsci12060770

AMA Style

Khare N, Maheshwari SK, Rizvi SMD, Albadrani HM, Alsagaby SA, Alturaiki W, Iqbal D, Zia Q, Villa C, Jha SK, Jha NK, Jha AK. Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease. Brain Sciences. 2022; 12(6):770. https://doi.org/10.3390/brainsci12060770

Chicago/Turabian Style

Khare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, Hind Muteb Albadrani, Suliman A. Alsagaby, Wael Alturaiki, Danish Iqbal, Qamar Zia, Chiara Villa, Saurabh Kumar Jha, Niraj Kumar Jha, and Abhimanyu Kumar Jha. 2022. "Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease" Brain Sciences 12, no. 6: 770. https://doi.org/10.3390/brainsci12060770

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