Deciphering the therapeutic role of Kigelia africana fruit in erectile dysfunction through metabolite profiling and molecular modelling

Informatics in Medicine Unlocked - Tập 37 - Trang 101190 - 2023
Femi Olawale1,2, Kolawole Olofinsan3, Oludare M. Ogunyemi4, Kayode O. Karigidi5, Gideon A. Gyebi6, Ibrahim M. Ibrahim7, Opeyemi Iwaloye8
1Department of Biochemistry, University of Lagos, Nigeria
2Department of Biochemistry, University of KwaZulu, South Africa
3Department of Biochemistry, Nile University of Nigeria, Nigeria
4Computational Biology and Biomolecular Modeling Laboratories, Department of Biochemistry, School of Basic Medical Sciences, Babcock University, Illishan-Remo, Ogun State, Nigeria
5Department of Biochemistry, Olusegun Agagu University of Science and Technology, Okitipupa, Nigeria
6Department of Biochemistry, Faculty of Science and Technology Bingham University, Karu, Nasarawa, Nigeria
7Department of Biophysics, Faculty of Sciences, Cairo University, Giza, Egypt
8Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Ondo State, P.M.B. 704, Akure, 360001, Nigeria

Tài liệu tham khảo

Oud, 2022, A de novo paradigm for male infertility, Nat Commun, 13, 1, 10.1038/s41467-021-27132-8 Gipson, 2020, Infertility: a continually neglected component of sexual and reproductive health and rights, Bull World Health Organ, 98, 505, 10.2471/BLT.20.252049 Sun, 2017, Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: results from a global burden of disease study, Aging (Albany NY), 11 Agarwal, 2021, Male infertility, Lancet, 397, 319, 10.1016/S0140-6736(20)32667-2 Yafi, 2016, Erectile dysfunction, Nat Rev Dis Prim, 2, 1 Andersson, 1995, Physiology of penile erection, Physiol Rev, 75, 191, 10.1152/physrev.1995.75.1.191 Burnett, 1995, Role of nitric oxide in the physiology of erection, Biol Reprod, 52, 485, 10.1095/biolreprod52.3.485 Chitaley, 2001, Antagonism of Rho-kinase stimulates rat penile erection via a nitric oxide-independent pathway, Nat Med, 7, 119, 10.1038/83258 Jin, 2006, Elevated RhoA/Rho‐kinase activity in the aged rat penis: mechanism for age‐associated erectile dysfunction, Faseb J, 20, 536, 10.1096/fj.05-4232fje Zewdie, 2020, A systematic review on rho-kinase as a potential therapeutic target for the treatment of erectile dysfunction, Res Rep Urol, 12, 261 Sopko, 2014, Understanding and targeting the Rho kinase pathway in erectile dysfunction, Nat Rev Urol, 11, 622, 10.1038/nrurol.2014.278 Uvin, 2017, Additive effects of the Rho kinase inhibitor Y‐27632 and vardenafil on relaxation of the corpus cavernosum tissue of patients with erectile dysfunction and clinical phosphodiesterase type 5 inhibitor failure, BJU Int, 119, 325, 10.1111/bju.13691 Renaud, 2002, Erectile-dysfunction therapies, Nat Rev Drug Discov, 1, 663, 10.1038/nrd898 Ryu, 2017, Research in pharmacotherapy for erectile dysfunction, Transl Androl Urol, 6, 207, 10.21037/tau.2016.11.17 Ding, 2017, Association of nNOS and Rho-kinase with age-associated erectile dysfunction in Sprague-Dawley rats, Exp Ther Med, 13, 1133, 10.3892/etm.2017.4064 Thoma, 2017, Too much ROCK—erection block, Nat Rev Urol, 14, 6, 10.1038/nrurol.2016.231 Albersen, 2010, The future is today: emerging drugs for the treatment of erectile dysfunction, Expet Opin Emerg Drugs, 15, 467, 10.1517/14728214.2010.480973 Hartmann, 2015, The function of Rho-associated kinases ROCK1 and ROCK2 in the pathogenesis of cardiovascular disease, Front Pharmacol, 6, 276, 10.3389/fphar.2015.00276 Goldstein, 2002, Oral sildenafil in the treatment of erectile dysfunction, J Urol, 167, 1197, 10.1016/S0022-5347(02)80386-X Vicari, 2005, Efficacy and safety of fasudil in patients with stable angina: a double-blind, placebo-controlled, phase 2 trial, J Am Coll Cardiol, 46, 1803, 10.1016/j.jacc.2005.07.047 Olofinsan, 2021, Ocimum tenuiflorum mitigates iron‐induced testicular toxicity via modulation of redox imbalance, cholinergic and purinergic dysfunctions, and glucose metabolizing enzymes activities, Andrologia, 53, 10.1111/and.14179 Nabatanzi, 2020, Ethnobotany, phytochemistry and pharmacological activity of kigelia africana (lam.) benth.(bignoniaceae), Plants, 9, 753, 10.3390/plants9060753 Fagbohun, 2021, Metabolite fingerprinting of ethyl acetate fraction of Kigelia africana fruit extracts: a comparison of chemical composition using GC–MS, GC-TOF-MS and UHPLC-TOF-MS/MS, Chem Data Collect, 31, 10.1016/j.cdc.2020.100623 Nabatanzi, 2020, Antioxidant and anti-inflammatory activities of kigelia africana (lam.) benth, Evidence-Based Complement Altern Med, 2020 Micheli, 2020, Effects of Kigelia africana (Lam.) Benth. fruits extract on the development and maturation of the reproductive system in immature male rats, Nat Prod Res, 34, 162, 10.1080/14786419.2019.1579809 Fagbohun, 2020, Metabolome modulatory effects of Kigelia africana (Lam.) Benth. fruit extracts on oxidative stress, hyperlipidaemic biomarkers in STZ-induced diabetic rats and antidiabetic effects in 3T3 L1 adipocytes, J Pharm Pharmacol, 72, 1798, 10.1111/jphp.13362 Iwaloye, 2020, Journal of computer science & in silico molecular studies of selected compounds as novel inhibitors for phosphodiesterase-5 (PDE5) in the management of erectile, Dysfunction, 13 Olawale, 2021, Virtual screening of natural compounds as selective inhibitors of polo-like kinase-1 at C-terminal polo box and N-terminal catalytic domain, J Biomol Struct Dyn, 1 Ogunyemi, 2022, Identification of promising multi-targeting inhibitors of obesity from Vernonia amygdalina through computational analysis, Mol Divers, 1–25 Ojo, 2021, Exploring the potentials of some compounds from Garcinia kola seeds towards identification of novel PDE‐5 inhibitors in erectile dysfunction therapy, Andrologia, 53, 10.1111/and.14092 Maryam, 2021, E-pharmacophore based virtual screening for identification of dual specific PDE5A and PDE3A inhibitors as potential leads against cardiovascular diseases, J Biomol Struct Dyn, 39, 2302, 10.1080/07391102.2020.1748718 Mali, 2021, Discovery of two novel hetero-tricyclic lead scaffolds as PDE5A inhibitor: virtual screening, molecular docking and pharmacophore modeling approach, Nat Prod Res, 35, 92, 10.1080/14786419.2019.1614582 Nandiyanto, 2019, How to read and interpret FTIR spectroscope of organic material, Indones J Sci Technol, 4, 97, 10.17509/ijost.v4i1.15806 Ma, 2010, Determination of phthalates in fruit jellies by dispersive SPE coupled with HPLC-MS, J Separ Sci, 33, 251, 10.1002/jssc.200900557 Pluskal, 2010, MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinf, 11, 395, 10.1186/1471-2105-11-395 Olasehinde, 2019, Phenolic composition, antioxidant activity, anticholinesterase potential and modulatory effects of aqueous extracts of some seaweeds on β-amyloid aggregation and disaggregation, Pharm Biol, 57, 460, 10.1080/13880209.2019.1634741 Guimarães, 2008, MM-GB/SA rescoring of docking poses in structure-based lead optimization, J Chem Inf Model, 48, 958, 10.1021/ci800004w Olawale, 2021, A multi-target approach for the discovery of anti breast cancer agents from plants secondary metabolites, Lett Drug Des Discov, 18, 1, 10.2174/1570180818666210521111535 Elekofehinti, 2021, Newly designed compounds from scaffolds of known actives as inhibitors of survivin: computational analysis from the perspective of fragment-based drug design, Silico Pharmacol, 9, 47, 10.1007/s40203-021-00108-8 Dixon, 2016, AutoQSAR: an automated machine learning tool for best-practice quantitative structure–activity relationship modeling, Future Med Chem, 8, 1825, 10.4155/fmc-2016-0093 Daina, 2017, SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules, Sci Rep, 7, 1, 10.1038/srep42717 Banerjee, 2018, ProTox-II: a webserver for the prediction of toxicity of chemicals, Nucleic Acids Res, 46, W257, 10.1093/nar/gky318 Jo, 2008, CHARMM‐GUI: a web‐based graphical user interface for CHARMM, J Comput Chem, 29, 1859, 10.1002/jcc.20945 Brooks, 2009, CHARMM: the biomolecular simulation program, J Comput Chem, 30, 1545, 10.1002/jcc.21287 Jo, 2014, Chapter eight - CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues, vol. 96, 235 Lee, 2016, CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field, J Chem Theor Comput, 12, 405, 10.1021/acs.jctc.5b00935 Abraham, 2015, GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers, Software, 1, 19, 10.1016/j.softx.2015.06.001 Bussi, 2007, Canonical sampling through velocity rescaling, J Chem Phys, 126, 10.1063/1.2408420 Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J Comput Chem, 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H Essmann, 1995, A smooth particle mesh Ewald method, J Chem Phys, 103, 8577, 10.1063/1.470117 Humphrey, 1996, VMD: visual molecular dynamics, J Mol Graph, 14, 33, 10.1016/0263-7855(96)00018-5 Tubiana, 2018, TTClust: a versatile molecular simulation trajectory clustering program with graphical summaries, J Chem Inf Model, 58, 2178, 10.1021/acs.jcim.8b00512 Salentin, 2015, PLIP: fully automated protein–ligand interaction profiler, Nucleic Acids Res, 43, W443, 10.1093/nar/gkv315 Miller, 2012, MMPBSA.py: an efficient program for end-state free energy calculations, J Chem Theor Comput, 8, 3314, 10.1021/ct300418h Valdés-Tresanco, 2021, gmx\_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS, J Chem Theor Comput, 17, 6281, 10.1021/acs.jctc.1c00645 Xue, 2018, What contributes to serotonin--norepinephrine reuptake inhibitors' dual-targeting mechanism? The key role of transmembrane domain 6 in human serotonin and norepinephrine transporters revealed by molecular dynamics simulation, ACS Chem Neurosci, 9, 1128, 10.1021/acschemneuro.7b00490 Tuccinardi, 2021, What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?, Expet Opin Drug Discov, 16, 1233, 10.1080/17460441.2021.1942836 Patle, 2020, Phytochemical screening and determination of phenolics and flavonoids in Dillenia pentagyna using UV–vis and FTIR spectroscopy, Spectrochim Acta Part A Mol Biomol Spectrosc, 242, 10.1016/j.saa.2020.118717 Arkhipov, 2014, Metabolomic profiling of kigelia africana extracts with anti-cancer activity by high resolution tandem mass spectroscopy, Pharmacogn Commun, 4 Oliveira, 2016, FTIR analysis and quantification of phenols and flavonoids of five commercially available plants extracts used in wound healing, Materia, 21, 767 Mbonyiryivuze, 2015 Costa, 2017, Phytochemical screening by LC-MS and LC-PDA of ethanolic extracts from the fruits of Kigelia africana (Lam.) Benth, Nat Prod Res, 31, 1397, 10.1080/14786419.2016.1253080 Moss, 1993, Sexual functioning of male anabolic steroid abusers, Arch Sex Behav, 22, 1, 10.1007/BF01552908 Olawale, 2022, Screening of compounds from Nigerian antidiabetic plants as protein tyrosine phosphatase 1B inhibitor, Comput Toxicol, 21, 10.1016/j.comtox.2021.100200 Ahmed, 2021, Phosphodiesterase 5 (PDE5): structure-function regulation and therapeutic applications of inhibitors, Biomed Pharmacother, 134, 10.1016/j.biopha.2020.111128 Lugnier, 2006, Cyclic nucleotide phosphodiesterase (PDE) superfamily: a new target for the development of specific therapeutic agents, Pharmacol Ther, 109, 366, 10.1016/j.pharmthera.2005.07.003 Sung, 2003, Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules, Nature, 425, 98, 10.1038/nature01914 Chung, 2020, Influence of GRK5 gene polymorphisms on ritodrine efficacy and adverse drug events in preterm labor treatment, Sci Rep, 10, 1 Gary, 2014, Ritodrine inhibits neuronal nitric oxide synthase, a potential link between tocolysis and autism, Med Chem Res, 23, 5102, 10.1007/s00044-014-1066-1 Huai, 2004, Crystal structures of phosphodiesterases 4 and 5 in complex with inhibitor 3-isobutyl-1-methylxanthine suggest a conformation determinant of inhibitor selectivity, J Biol Chem, 279, 13095, 10.1074/jbc.M311556200 Ahinko, 2019, Suitability of MMGBSA for the selection of correct ligand binding modes from docking results, Chem Biol Drug Des, 93, 522, 10.1111/cbdd.13446 Maffucci, 2018, An efficient implementation of the Nwat-MMGBSA method to rescore docking results in medium-throughput virtual screenings, Front Chem, 6, 43, 10.3389/fchem.2018.00043 Ekins, 2009, Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR, PLoS Comput Biol, 5, 10.1371/journal.pcbi.1000594 Pinzi, 2019, Molecular docking: shifting paradigms in drug discovery, Int J Mol Sci, 20, 4331, 10.3390/ijms20184331 Cho, 2009, Extension of QM/MM docking and its applications to metalloproteins, J Comput Chem, 30, 2609, 10.1002/jcc.21270 Schneider, 2016, Spotting and designing promiscuous ligands for drug discovery, Chem Commun, 52, 1135, 10.1039/C5CC07506H Lin, 2003, Role of P-glycoprotein in pharmacokinetics, Clin Pharmacokinet, 42, 59, 10.2165/00003088-200342010-00003 Shen, 2010, Estimation of ADME properties with substructure pattern recognition, J Chem Inf Model, 50, 1034, 10.1021/ci100104j Okimoto, 2009, High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations, PLoS Comput Biol, 5, 10.1371/journal.pcbi.1000528 Dong, 2018, Structural flexibility and protein adaptation to temperature: molecular dynamics analysis of malate dehydrogenases of marine molluscs, Proc Natl Acad Sci USA, 115, 1274, 10.1073/pnas.1718910115 Olawale, 2022, Homology modelling, vHTS, pharmacophore, molecular docking and molecular dynamics studies for the identification of natural compound-derived inhibitor of MRP3 in acute leukaemia treatment, Chem Pap, 76, 3729, 10.1007/s11696-022-02128-w Sinha, 2020, Classification of VUS and unclassified variants in BRCA1 BRCT repeats by molecular dynamics simulation, Comput Struct Biotechnol J, 18, 723, 10.1016/j.csbj.2020.03.013