Psychoactive Plant Database - Neuroactive Phytochemical Collection

1. J Cell Biochem. 2024 Jul;125(7):e30611. doi: 10.1002/jcb.30611. Epub 2024 Jun 
17.

In Silico Prediction of Potential Inhibitors for Targeting RNA CAG Repeats via 
Molecular Docking and Dynamics Simulation: A Drug Discovery Approach.

Singh S(1), Singh S(1), Joshi D(2), Mohanty C(1), Singh R(1).

Author information:
(1)Department of Anatomy, Institute of Medical Sciences, Banaras Hindu 
University, Varanasi, Uttar Pradesh, India.
(2)Department of Neurology, Institute of Medical Sciences, Banaras Hindu 
University, Varanasi, Uttar Pradesh, India.

Spinocerebellar ataxia (SCA) is a rare neurological illness inherited dominantly 
that causes severe impairment and premature mortality. While each rare disease 
may affect individuals infrequently, collectively they pose a significant 
healthcare challenge. It is mainly carried out due to the expansion of RNA 
triplet (CAG) repeats, although missense or point mutations can also be induced. 
Unfortunately, there is no cure; only symptomatic treatments are available. To 
date, SCA has about 48 subtypes, the most common of these being SCA 1, 2, 3, 6, 
7, 12, and 17 having CAG repeats. Using molecular docking and molecular dynamics 
(MD) simulation, this study seeks to investigate effective natural herbal 
neuroprotective compounds against CAG repeats, which are therapeutically 
significant in treating SCA. Initially, virtual screening followed by molecular 
docking was used to estimate the binding affinity of neuroprotective natural 
compounds toward CAG repeats. The compound with the highest binding affinity, 
somniferine, was then chosen for MD simulation. The structural stability, 
interaction mechanism, and conformational dynamics of CAG repeats and 
somniferine were investigated via MD simulation. The MD study revealed that 
during the simulation period, the interaction between CAG repeats and 
somniferine stabilizes and results in fewer conformational variations. This in 
silico study suggests that Somniferine can be used as a therapeutic medication 
against RNA CAG repeats in SCA.

© 2024 Wiley Periodicals LLC.

DOI: 10.1002/jcb.30611
PMID: 38884365 [Indexed for MEDLINE]


2. Front Cell Infect Microbiol. 2022 Aug 15;12:933824. doi: 
10.3389/fcimb.2022.933824. eCollection 2022.

Withania somnifera (L.) Dunal (Ashwagandha) for the possible therapeutics and 
clinical management of SARS-CoV-2 infection: Plant-based drug discovery and 
targeted therapy.

Singh M(1)(2), Jayant K(3), Singh D(2), Bhutani S(1), Poddar NK(4), Chaudhary 
AA(5), Khan SU(6), Adnan M(7), Siddiqui AJ(7), Hassan MI(8), Khan FI(9)(10), Lai 
D(10), Khan S(11)(12)(13).

Author information:
(1)Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, 
India.
(2)Department of Biochemistry, C.B.S.H, G.B Pant University of Agriculture and 
Technology, Pantnagar, Uttrakhand, India.
(3)Department of Agricultural and Food Engineering, IIT Kharagpur, West Bengal, 
Kharagpur, India.
(4)Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, 
India.
(5)Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic 
University, Riyadh, Saudi Arabia.
(6)Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud 
Islamic University (IMSIU), Riyadh, Saudi Arabia.
(7)Department of Biology, College of Science, University of Hail, Hail, Saudi 
Arabia.
(8)Center for Interdisciplinary Research in Basic Sciences, Jamia Millia 
Islamia, New Delhi, India.
(9)Department of Biological Sciences, School of Science, Xi'an 
Jiaotong-Liverpool University, Suzhou, China.
(10)School of Electronic Science and Engineering, University of Electronic 
Science and Technology of China, Chengdu, China.
(11)Department of Health Sciences, Novel Global Community Educational Foundation 
7 Peterlee Place, Hebersham, NSW, Australia.
(12)Department of Medical Lab Technology, Indian Institute of Health and 
Technology (IIHT), Deoband, Saharanpur, UP, India.
(13)Department of Pharmaceutics, College of Pharmacy, King Saud University, 
Riyadh, Saudi Arabia.

Coronavirus disease 2019 (COVID-19) pandemic has killed huge populations 
throughout the world and acts as a high-risk factor for elderly and young 
immune-suppressed patients. There is a critical need to build up secure, 
reliable, and efficient drugs against to the infection of severe acute 
respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Bioactive compounds of 
Ashwagandha [Withania somnifera (L.) Dunal] may implicate as herbal medicine for 
the management and treatment of patients infected by SARS-CoV-2 infection. The 
aim of the current work is to update the knowledge of SARS-CoV-2 infection and 
information about the implication of various compounds of medicinal plant 
Withania somnifera with minimum side effects on the patients' organs. The herbal 
medicine Withania somnifera has an excellent antiviral activity that could be 
implicated in the management and treatment of flu and flu-like diseases 
connected with SARS-CoV-2. The analysis was performed by systematically 
re-evaluating the published articles related to the infection of SARS-CoV-2 and 
the herbal medicine Withania somnifera. In the current review, we have provided 
the important information and data of various bioactive compounds of Withania 
somnifera such as Withanoside V, Withanone, Somniferine, and some other 
compounds, which can possibly help in the management and treatment of SARS-CoV-2 
infection. Withania somnifera has proved its potential for maintaining immune 
homeostasis of the body, inflammation regulation, pro-inflammatory cytokines 
suppression, protection of multiple organs, anti-viral, anti-stress, and 
anti-hypertensive properties. Withanoside V has the potential to inhibit the 
main proteases (Mpro) of SARS-CoV-2. At present, synthetic adjuvant vaccines are 
used against COVID-19. Available information showed the antiviral activity in 
Withanoside V of Withania somnifera, which may explore as herbal medicine 
against to SARS-CoV-2 infection after standardization of parameters of drug 
development and formulation in near future.

Copyright © 2022 Singh, Jayant, Singh, Bhutani, Poddar, Chaudhary, Khan, Adnan, 
Siddiqui, Hassan, Khan, Lai and Khan.

DOI: 10.3389/fcimb.2022.933824
PMCID: PMC9421373
PMID: 36046742 [Indexed for MEDLINE]

Conflict of interest statement: The authors declare that the research was 
conducted in the absence of any commercial or financial relationships that could 
be construed as a potential conflict of interest.


3. Saudi J Biol Sci. 2022 Apr;29(4):2432-2446. doi: 10.1016/j.sjbs.2021.12.018. 
Epub 2021 Dec 13.

Repurposing of phytomedicine-derived bioactive compounds with promising 
anti-SARS-CoV-2 potential: Molecular docking, MD simulation and 
drug-likeness/ADMET studies.

Rudrapal M(1), Gogoi N(2), Chetia D(2), Khan J(3)(4), Banwas S(3)(4)(5), 
Alshehri B(3)(4), Alaidarous MA(3)(4), Laddha UD(6), Khairnar SJ(6), Walode 
SG(1).

Author information:
(1)Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of 
Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, 
India.
(2)Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 
786004, Assam, India.
(3)Department of Medical Laboratory Sciences, College of Applied Medical 
Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia.
(4)Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 
11952, Saudi Arabia.
(5)Department of Biomedical Sciences, Oregon State University, Corvallis, OR 
97331, USA.
(6)MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, 
Maharashtra, India.

In view of the potential of traditional plant-based remedies (or phytomedicines) 
in the management of COVID-19, the present investigation was aimed at finding 
novel anti-SARS-CoV-2 molecules by in silico screening of bioactive 
phytochemicals (database) using computational methods and drug repurposing 
approach. A total of 160 compounds belonging to various phytochemical classes 
(flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected 
(as initial hits) and screened against three specific therapeutic targets 
(Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics 
simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals 
were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with 
promising inhibitory effects effective against protease (Mpro and PLpro) and 
polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, 
saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. 
On the basis of binding modes and dynamics studies of protein-ligand 
intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the 
most potent (in silico) inhibitors potentially active against Mpro, PLpro and 
RdRp, respectively. The present investigation can be directed towards further 
experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with 
toxicities of identified phytomolecules.

© 2021 The Author(s).

DOI: 10.1016/j.sjbs.2021.12.018
PMCID: PMC8667520
PMID: 34924801

Conflict of interest statement: The authors declare that they have no known 
competing financial interests or personal relationships that could have appeared 
to influence the work reported in this paper.


4. Molecules. 2021 Sep 21;26(18):5724. doi: 10.3390/molecules26185724.

In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors 
against Main Protease and the Receptor-Binding Domain of SARS-CoV-2.

Mousavi SS(1), Karami A(1), Haghighi TM(1), Tumilaar SG(2), Fatimawali(2)(3), 
Idroes R(4), Mahmud S(5), Celik I(6), Ağagündüz D(7), Tallei TE(3)(8), Emran 
TB(9), Capasso R(10).

Author information:
(1)Department of Horticultural Science, School of Agriculture, Shiraz 
University, Shiraz 71441, Iran.
(2)Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam 
Ratulangi University, Manado 95115, Indonesia.
(3)The University Center of Excellence for Biotechnology and Conservation of 
Wallacea, Sam Ratulangi University, Manado 95115, Indonesia.
(4)Department of Pharmacy, Faculty of Mathematics and Natural Sciences, 
Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia.
(5)Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, 
University of Rajshahi, Rajshahi 6205, Bangladesh.
(6)Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes 
University, Kayseri 38039, Turkey.
(7)Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi 
University, Emek, Ankara 06490, Turkey.
(8)Department of Biology, Faculty of Mathematics and Natural Sciences, Sam 
Ratulangi University, Manado 95115, Indonesia.
(9)Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, 
Bangladesh.
(10)Department of Agricultural Sciences, University of Naples Federico II, 
Portici, 80055 Naples, Italy.

The novel coronavirus disease 2019 (COVID-19) is caused by the severe acute 
respiratory syndrome coronavirus 2 (SARS-CoV-2), which initially appeared in 
Wuhan, China, in December 2019. Elderly individuals and those with comorbid 
conditions may be more vulnerable to this disease. Consequently, several 
research laboratories continue to focus on developing drugs to treat this 
infection because this disease has developed into a global pandemic with an 
extremely limited number of specific treatments available. Natural herbal 
remedies have long been used to treat illnesses in a variety of cultures. Modern 
medicine has achieved success due to the effectiveness of traditional medicines, 
which are derived from medicinal plants. The objective of this study was to 
determine whether components of natural origin from Iranian medicinal plants 
have an antiviral effect that can prevent humans from this coronavirus infection 
using the most reliable molecular docking method; in our case, we focused on the 
main protease (Mpro) and a receptor-binding domain (RBD). The results of 
molecular docking showed that among 169 molecules of natural origin from common 
Iranian medicinal plants, 20 molecules (chelidimerine, rutin, fumariline, 
catechin gallate, adlumidine, astragalin, somniferine, etc.) can be proposed as 
inhibitors against this coronavirus based on the binding free energy and type of 
interactions between these molecules and the studied proteins. Moreover, a 
molecular dynamics simulation study revealed that the chelidimerine-Mpro and 
somniferine-RBD complexes were stable for up to 50 ns below 0.5 nm. Our results 
provide valuable insights into this mechanism, which sheds light on future 
structure-based designs of high-potency inhibitors for SARS-CoV-2.

DOI: 10.3390/molecules26185724
PMCID: PMC8470205
PMID: 34577194 [Indexed for MEDLINE]

Conflict of interest statement: The authors declare no conflict of interest.


5. J Biomol Struct Dyn. 2022 Jan;40(1):190-203. doi:
10.1080/07391102.2020.1810778.  Epub 2020 Aug 27.

Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of 
ayurvedic medicinal plants - Withania somnifera (Ashwagandha), Tinospora 
cordifolia (Giloy) and Ocimum sanctum (Tulsi) - a molecular docking study.

Shree P(1), Mishra P(1), Selvaraj C(2), Singh SK(2), Chaube R(3), Garg N(1), 
Tripathi YB(1).

Author information:
(1)Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras 
Hindu University, Varanasi, India.
(2)Computer Aided Drug Design and Molecular Modeling Lab, Department of 
Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamilnadu, India.
(3)Department of Zoology, Institute of Science, Banaras Hindu University, 
Varanasi, India.

COVID-19 (Coronavirus disease 2019) is a transmissible disease initiated and 
propagated through a new virus strain SARS-CoV-2 (Severe Acute Respiratory 
Syndrome Coronavirus-2) since 31st December 2019 in Wuhan city of China and the 
infection has outspread globally influencing millions of people. Here, an 
attempt was made to recognize natural phytochemicals from medicinal plants, in 
order to reutilize them against COVID-19 by the virtue of molecular docking and 
molecular dynamics (MD) simulation study. Molecular docking study showed six 
probable inhibitors against SARS-CoV-2 Mpro (Main protease), two from Withania 
somnifera (Ashwagandha) (Withanoside V [10.32 kcal/mol] and Somniferine 
[9.62 kcal/mol]), one from Tinospora cordifolia (Giloy) (Tinocordiside 
[8.10 kcal/mol]) and three from Ocimum sanctum (Tulsi) (Vicenin [8.97 kcal/mol], 
Isorientin 4'-O-glucoside 2″-O-p-hydroxybenzoagte [8.55 kcal/mol] and Ursolic 
acid [8.52 kcal/mol]). ADMET profile prediction showed that the best docked 
phytochemicals from present work were safe and possesses drug-like properties. 
Further MD simulation study was performed to assess the constancy of docked 
complexes and found stable. Hence from present study it could be suggested that 
active phytochemicals from medicinal plants could potentially inhibit Mpro of 
SARS-CoV-2 and further equip the management strategy against COVID-19-a global 
contagion. HighlightsHolistic approach of Ayurvedic medicinal plants to avenge 
against COVID-19 pandemic.Active phytoconstituents of Ayurvedic medicinal plants 
Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum 
sanctum (Tulsi) predicted to significantly hinder main protease (Mpro or 3Clpro) 
of SARS-CoV-2.Through molecular docking and molecular dynamic simulation study, 
Withanoside V, Somniferine, Tinocordiside, Vicenin, Ursolic acid and Isorientin 
4'-O-glucoside 2″-O-p-hydroxybenzoagte were anticipated to impede the activity 
of SARS-CoV-2 Mpro.Drug-likeness and ADMET profile prediction of best docked 
compounds from present study were predicted to be safe, drug-like compounds with 
no toxicity.Communicated by Ramaswamy H. Sarma.

DOI: 10.1080/07391102.2020.1810778
PMCID: PMC7484581
PMID: 32851919 [Indexed for MEDLINE]

Conflict of interest statement: No potential conflict of interest was reported 
by the author(s).