TY - JOUR
T1 - Computational Lock and Key and Dynamic Trajectory Analysis of Natural Biophors Against COVID-19 Spike Protein to Identify Effective Lead Molecules
AU - Navabshan, Irfan
AU - Sakthivel, Balasubramaniyan
AU - Pandiyan, Rajesh
AU - Antoniraj, Mariya Gover
AU - Dharmaraj, Selvakumar
AU - Ashokkumar, Veeramuthu
AU - Khoo, Kuan Shiong
AU - Chew, Kit Wayne
AU - Sugumaran, Abimanyu
AU - Show, Pau Loke
N1 - Funding Information:
The authors are thanking full to SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, National Centre for Coastal Research (NCCR), Chennai and Karpagam Academy of Higher Education, Coimbatore and Alagappa University, Karaikudi-630003, India.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2021/10
Y1 - 2021/10
N2 - New pandemic infection of coronaviridae family virus spread to more than 210 countries with total infection of 1,136,851 and 62,955 (4.6%) deaths until 5th April 2020. Which stopped the regular cycle of humankind but the nature is consistently running. There is no micro molecule remedy found yet to restore the regular life of people. Hence, we decided to work on natural biophores against the COVID proteins. As a first step, major phytoconstituents of antiviral herbs like Leucas aspera, Morinda citrifolia, Azadirachta indica, Curcuma longa, Piper nigrum, Ocimum tenuiflorum, and Corallium rubrum collected and performed the lock and key analysis with major spike protein of COVID-19 to find the best fitting lead biophore using computational drug design platform. The results of protocol run showed, phytoconstituents of Morinda citrifolia and Leucas aspera were found lower binding energy range of − 55.18 to − 25.34 kcal/mol, respectively and compared with Hydroxychloroquine (HCQ) (− 24.29 kcal/mol) and Remdesivir (− 25.38 kcal/mol). The results conclude that, core skeletons chromen, anthracene 9, 11 dione and long-chain alkyl acids/ester-containing biophores showen high stable antagonistic affinity with S-protein. Which leads the breakdown of spike protein and ACE2 receptor complex formation and host mechanism of corono virus. In addition, the dynamic trajectory analysis confirmed the complete denaturation of spike protein by the molecule 4-(24-hydroxy-1-oxo-5-n-propyltetracosanyl)-phenol from Leucas aspera and stability of spike-ligand complex. These biophores will aid the researcher to fabricate new promising analogue and being recommended to assess its COVID-19 treatment.
AB - New pandemic infection of coronaviridae family virus spread to more than 210 countries with total infection of 1,136,851 and 62,955 (4.6%) deaths until 5th April 2020. Which stopped the regular cycle of humankind but the nature is consistently running. There is no micro molecule remedy found yet to restore the regular life of people. Hence, we decided to work on natural biophores against the COVID proteins. As a first step, major phytoconstituents of antiviral herbs like Leucas aspera, Morinda citrifolia, Azadirachta indica, Curcuma longa, Piper nigrum, Ocimum tenuiflorum, and Corallium rubrum collected and performed the lock and key analysis with major spike protein of COVID-19 to find the best fitting lead biophore using computational drug design platform. The results of protocol run showed, phytoconstituents of Morinda citrifolia and Leucas aspera were found lower binding energy range of − 55.18 to − 25.34 kcal/mol, respectively and compared with Hydroxychloroquine (HCQ) (− 24.29 kcal/mol) and Remdesivir (− 25.38 kcal/mol). The results conclude that, core skeletons chromen, anthracene 9, 11 dione and long-chain alkyl acids/ester-containing biophores showen high stable antagonistic affinity with S-protein. Which leads the breakdown of spike protein and ACE2 receptor complex formation and host mechanism of corono virus. In addition, the dynamic trajectory analysis confirmed the complete denaturation of spike protein by the molecule 4-(24-hydroxy-1-oxo-5-n-propyltetracosanyl)-phenol from Leucas aspera and stability of spike-ligand complex. These biophores will aid the researcher to fabricate new promising analogue and being recommended to assess its COVID-19 treatment.
KW - Anthracene 9,11 dione
KW - COVID-19
KW - Dynamic simulation
KW - In-silico method
KW - Natural Biophors
KW - Spike Protein
UR - http://www.scopus.com/inward/record.url?scp=85115037726&partnerID=8YFLogxK
U2 - 10.1007/s12033-021-00358-z
DO - 10.1007/s12033-021-00358-z
M3 - Review article
C2 - 34159564
AN - SCOPUS:85115037726
SN - 1073-6085
VL - 63
SP - 898
EP - 908
JO - Molecular Biotechnology
JF - Molecular Biotechnology
IS - 10
ER -