Inhibitory effects of selected isoquinoline alkaloids against main protease (Mpro) of SARS-CoV-2, in silico study

Alamri MA, Tahir Ul Qamar M, Mirza MU, Bhadane R, Alqahtani SM, Muneer I et al (2020) Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro. J Biomol Struct Dyn 39:4936–4948

Banerjee P, Eckert AO, Schrey AK, Preissner R (2018) ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res 46:W257–W263

Behbahani M, Moradi M, Mohabatkar H (2021) In silico design of a multi-epitope peptide construct as a potential vaccine candidate for Influenza A based on neuraminidase protein. In Silico Pharmacol 9:1–13

Bentley KW (2001) β-Phenylethylamines and the isoquinoline alkaloids. Nat Prod Rep 18:148–170

Borquaye LS, Gasu EN, Ampomah GB, Kyei LK, Amarh MA, Mensah CN et al (2020) Alkaloids from Cryptolepis sanguinolenta as potential inhibitors of SARS-CoV-2 viral proteins: an in silico study. BioMed Res Int. https://doi.org/10.1155/2020/5324560

Cao X (2020) COVID-19: immunopathology and its implications for therapy. Nat Rev Immunol 20:269–270

Cao B, Wang Y, Wen D, Liu W, Wang J, Fan G et al (2020) A trial of lopinavir–ritonavir in adults hospitalized with severe Covid-19. New Engl J Med 382:1787–1799

Chakravarti R, Singh R, Ghosh A, Dey D, Sharma P, Velayutham R et al (2021) A review on potential of natural products in the management of COVID-19. RSC Adv 11:16711–16735

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y et al (2020) Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395:507–513

Chinsembu KC (2019) Chemical diversity and activity profiles of HIV-1 reverse transcriptase inhibitors from plants. Rev Bras 29:504–528

Cortegiani A, Ingoglia G, Ippolito M, Giarratano A, Einav S (2020) A systematic review on the efficacy and safety of chloroquine for the treatment of COVID-19. J Crit Care 57:279–283

Da C, Gu X, Pei G (2015) 5-Phytochemical and biological research of Chelidonieae pharmaceutical resources. Medicinal plants chemistry, biology and omics. Woodhead Publishing, Cambridge, pp 171–216

Daina A, Michielin O, Zoete V (2017a) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:1–13

Daina A, Michielin O, Zoete V (2017b) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717

Dey P, Kundu A, Kumar A, Gupta M, Lee BM, Bhakta T et al (2020) Analysis of alkaloids (indole alkaloids, isoquinoline alkaloids, tropane alkaloids). Recent advances in natural products analysis. Elsevier, Amsterdam, pp 505–567

Diamond A, Desgagné-Penix I (2016) Metabolic engineering for the production of plant isoquinoline alkaloids. Plant Biotechnol J 14:1319–1328

Enmozhi SK, Raja K, Sebastine I, Joseph J (2020) Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2020.1760136

Garg S, Roy A (2020) In silico analysis of selected alkaloids against main protease (Mpro) of SARS-CoV-2. Chemico-Biol Interact 332:1009309

Georgiev V, Ivanov I, Berkov S, Ilieva M, Georgiev M, Gocheva T et al (2012) Galanthamine production by L. eucojum L. aestivum shoot culture in a modified bubble column bioreactor with internal sections. Eng Life Sci 12:534–543

Gyebi GA, Ogunro OB, Adegunloye AP, Ogunyemi OM, Afolabi SO (2021) Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants. J Biomol Struct Dyn 39:3396–3408

Heh CH, Othman R, Buckle MJ, Sharifuddin Y, Yusof R, Rahman NA (2013) Rational discovery of dengue type 2 non-competitive inhibitors. Chem Biol Drug Des 82:1–11

Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y et al (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582:289–293

Joshi T, Sharma P, Joshi T, Pundir H, Mathpal S, Chandra S (2020) Structure-based screening of novel lichen compounds against SARS Coronavirus main protease (Mpro) as potentials inhibitors of COVID-19. Mol Divers. https://doi.org/10.1007/s11030-020-10118-x

Kar P, Kumar V, Vellingiri B, Sen A, Jaishee N, Anandraj A et al (2020) Anisotine and amarogentin as promising inhibitory candidates against SARS-CoV-2 proteins: a computational investigation. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2020.1860133

Khaerunnisa S, Kurniawan H, Awaluddin R, Suhartati S (2020) Potential inhibitor of COVID-19 main Protease (M pro) from several medicinal plant compounds by molecular docking study. Preprints. https://doi.org/10.20944/preprints202003.0226.v1

Kiffer-Moreira T, Sheen CR, da Silva Gasque KC, Bolean M, Ciancaglini P, van Elsas A et al (2014) Catalytic signature of a heat-stable, chimeric human alkaline phosphatase with therapeutic potential. PLoS ONE 9:e89374

Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A et al (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213

Kukula-Koch W, Widelski J (2017) Alkaloids. Pharmacognosy. Elsevier, Amsterdam, pp 163–198

Kumar N, Awasthi A, Kumari A, Sood D, Jain P, Singh T et al (2020) Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis. J Biomol Struct Dyn 40:101–116

Li Z, Li X, Huang Y-Y, Wu Y, Liu R, Zhou L et al (2020) Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs. Proc Natl Acad Sci 117:27381–27387

Mahmud S, Biswas S, Paul GK, Mita MA, Promi MM, Afrose S et al (2021) Plant-based phytochemical screening by targeting main protease of SARS-CoV-2 to design effective potent inhibitors. Biology 10:589

Mark P, Nilsson L (2001) Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J Phys Chem A 105:9954–9960

Modarresi M, Chahardoli A, Karimi N, Chahardoli S (2020) Variations of glaucine, quercetin and kaempferol contents in Nigella arvensis against Al2O3, NiO, and TiO2 nanoparticles. Heliyon 6:e04265

Mombelli E, Raitano G, Benfenati E (2016) In silico prediction of chemically induced mutagenicity: how to use QSAR models and interpret their results. In silico methods for predicting drug toxicity. Springer, Berlin, pp 87–105

Mpiana PT, Tshibangu DS, Kilembe JT, Gbolo BZ, Mwanangombo DT, Inkoto CL et al (2020) Identification of potential inhibitors of SARS-CoV-2 main protease from Aloe vera compounds: a molecular docking study. Chem Phys Lett 754:751

Narkhede RR, Pise AV, Cheke RS, Shinde SD (2020) Recognition of natural products as potential inhibitors of COVID-19 main protease (Mpro): In-silico evidences. Natl Prod Bioprospecting 10:297–306

Orhan I, Özçelik B, Karaoğlu T, Şener B (2007) Antiviral and antimicrobial profiles of selected isoquinoline alkaloids from Fumaria and Corydalis species. Z Für Naturforschung C 62:19–26

Paraiso IL, Revel JS, Stevens JF (2020) Potential use of polyphenols in the battle against COVID-19. Curr Opin Food Sci. https://doi.org/10.1016/j.cofs.2020.08.004

Rodríguez-Morales AJ, MacGregor K, Kanagarajah S, Patel D, Schlagenhauf P (2020) Going global–travel and the 2019 novel coronavirus. Travel Med Infect Dis 33:1078

Sadeghi M, Zarei MA (2020) Molecular docking studies of some flavone analogues as α-Glucosidase inhibitors. J Med Plants 19:55–64

Sadeghi M, Miroliaei M, Shorakai Z (2021a) In silico investigation of flavanone compounds’ inhibitory effects on alpha-amylase enzyme and predicting their inhibitory role in diabetes progression. J Fasa Univ Med Sci 10:2786–2795

Sadeghi M, Moradi M, Madanchi H, Johari B (2021b) In silico study of garlic (Allium sativum L.)-derived compounds molecular interactions with α-glucosidase. In Silico Pharmacol 9:11

Sadeghi M, Miroliaei M, Fateminasab F, Moradi M (2022) Screening cyclooxygenase-2 inhibitors from Allium sativum L. compounds: in silico approach. J Mol Model 28:1–12

Sneha P, Doss CGP (2016) Molecular dynamics: new frontier in personalized medicine. Advances in protein chemistry and structural biology, 102nd edn. Elsevier, Amsterdam, pp 181–224

Thirumal KD, Lavanya P, George PDC, Tayubi IA, Naveen KD, Francis YI et al (2017) A molecular docking and dynamics approach to screen potent inhibitors against fosfomycin resistant enzyme in clinical klebsiella pneumoniae. J Cell Biochem 118:4088–4094

Uddin M, Mustafa F, Rizvi TA, Loney T, Suwaidi HA, Al-Marzouqi AHH et al (2020) SARS-CoV-2/COVID-19: Viral genomics, epidemiology, vaccines, and therapeutic interventions. Viruses 12:526

Velavan TP, Meyer CG (2020) The COVID-19 epidemic. Trop Med Int Health 25:278

Walters WP (2012) Going further than Lipinski’s rule in drug design. Expert Opin Drug Discov 7:99–107

Wu JT, Leung K, Leung GM (2020) Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study. Lancet 395:689–697

Zhao Q, Zhao Y, Wang K (2006) Antinociceptive and free radical scavenging activities of alkaloids isolated from Lindera angustifolia Chen. J Ethnopharmacol 106:408–413

Zhu YC, Yao J, Adamczyk J, Luttrell R (2017) Feeding toxicity and impact of imidacloprid formulation and mixtures with six representative pesticides at residue concentrations on honey bee physiology (Apis mellifera). PLoS ONE 12:e0178421