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Ja’afaru SC, Uzairu A, Bayil I, Sallau MS, Ndukwe GI, Ibrahim MT, Moin AT, Mollah AKMM, Absar N. Unveiling potent inhibitors for schistosomiasis through ligand-based drug design, molecular docking, molecular dynamics simulations and pharmacokinetics predictions. PLoS One 2024; 19:e0302390. [PMID: 38923997 PMCID: PMC11207139 DOI: 10.1371/journal.pone.0302390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 06/28/2024] Open
Abstract
Schistosomiasis is a neglected tropical disease which imposes a considerable and enduring impact on affected regions, leading to persistent morbidity, hindering child development, diminishing productivity, and imposing economic burdens. Due to the emergence of drug resistance and limited management options, there is need to develop additional effective inhibitors for schistosomiasis. In view of this, quantitative structure-activity relationship studies, molecular docking, molecular dynamics simulations, drug-likeness and pharmacokinetics predictions were applied to 39 Schistosoma mansoni Thioredoxin Glutathione Reductase (SmTGR) inhibitors. The chosen QSAR model demonstrated robust statistical parameters, including an R2 of 0.798, R2adj of 0.767, Q2cv of 0.681, LOF of 0.930, R2test of 0.776, and cR2p of 0.746, confirming its reliability. The most active derivative (compound 40) was identified as a lead candidate for the development of new potential non-covalent inhibitors through ligand-based design. Subsequently, 12 novel compounds (40a-40l) were designed with enhanced anti-schistosomiasis activity and binding affinity. Molecular docking studies revealed strong and stable interactions, including hydrogen bonding, between the designed compounds and the target receptor. Molecular dynamics simulations over 100 nanoseconds and MM-PBSA free binding energy (ΔGbind) calculations validated the stability of the two best-designed molecules. Furthermore, drug-likeness and pharmacokinetics prediction analyses affirmed the potential of these designed compounds, suggesting their promise as innovative agents for the treatment of schistosomiasis.
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Affiliation(s)
- Saudatu Chinade Ja’afaru
- Department of Chemistry Ahmadu Bello University Zaria, Zaria, Nigeria
- Department of Chemistry, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Imren Bayil
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | | | | | | | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
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2
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Anyubaga SB, Shallangwa GA, Uzairu A, Abechi SE. Chemo-informatics applications in the design of novel 7-keto-sempervirol derivatives as SmCB1 inhibitors with potential for treatment of Schistosomiasis. Heliyon 2024; 10:e23115. [PMID: 38173516 PMCID: PMC10761359 DOI: 10.1016/j.heliyon.2023.e23115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The quest for a sound treatment on the vulnerable population suffering and dying as a result of the blood flukes, S. mansoni is on the increase because both Praziquantel and Oxamniquine widely used for the treatment of Schistosomiasis for over 51 years suffer resistance and recurrence. Here-in, chemo-informatics techniques such as QSAR modeling, pharmacokinetic, docking alongside MD simulation were harnessed in designing novel 7-keto- sempevirolsempevirol derivatives that are more competent against S. mansoni. Upon QSAR screening, compound 15, which appears to be in the model's acceptability space, emerges the best with a high predicted activity. 5 new analogues with improved activity against Schistosomiasis better than the standard drug PZQ were designed from compound 15 (template 15*) on an account of the descriptors significance from the model with robust and validated parameters. Also their pharmacokinetic profiles indicates that the designed compounds have the characteristics of a good drug. Furthermore, docking evaluation fulfilled ranges from -113.121 to -100.79 kcal/mol (moldock score), with compound U1 being the best (least moldock score of -113.121 compared to PZQ and 15* (template) having a moldock score value of (-87.21 and -83.37 kcal/mol). 100-ns MD Simulation on the U1-docked complex was run using Desmond 2019-4 package. The nature and steadiness of U1 compound within the enzyme active site was further confirmed by RMSD, RMSF, RoG and H-bond assessment. Hence, we recommend compound U1 targeting the SmCB1 enzyme (6YI7) for Schistosomiasis treatment and for further medicinal evaluation and utilization.
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Affiliation(s)
| | | | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University, P.M.B. 1044, Zaria, Nigeria
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Kumar RN, Prasanth D, Midthuri PG, Ahmad SF, Badarinath AV, Karumanchi SK, Seemaladinne R, Nalluri R, Pasala PK. Unveiling the Cardioprotective Power: Liquid Chromatography-Mass Spectrometry (LC-MS)-Analyzed Neolamarckia cadamba (Roxb.) Bosser Leaf Ethanolic Extract against Myocardial Infarction in Rats and In Silico Support Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3722. [PMID: 37960078 PMCID: PMC10650531 DOI: 10.3390/plants12213722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Neolamarckia cadamba (Roxb.) Bosser, a member of the Rubiaceae family, is a botanical species with recognized therapeutic properties. It is commonly used in traditional medicine to treat cardiac ailments and other disorders. However, the precise active constituents and the potential mechanisms by which they manage cardiovascular disorders remain unclear. Therefore, this study aimed to ascertain the bioactive components and investigate their underlying mechanisms of action. N. cadamba is used to treat cardiovascular disorders using the integrated metabolomic methodology. An HPLC-QTOF-MS/MS analysis determined the potential chemicals in the N. cadamba leaf ethanol extract (NCEE). A thorough investigation of the NCEE samples used in this study led to the identification of 32 phytoconstituents. Of the 32 compounds, 19 obeyed Lipinski's rule of five (RO5). A molecular docking study directed towards HMG-CoA reductase used 19 molecules. The reference drug atorvastatin indicated a binding energy of -3.9 kcal/mol, while the other substances, Cinchonain Ib and Dukunolide B, revealed binding energies of -5.7 and -5.3 kcal/mol, respectively. Both phytocompounds showed no toxicity and exhibited favorable pharmacokinetic properties. In vivo study results concluded that treatment with NCEE significantly reduced the cardiac myocardial infarction (MI) marker CK-MB and atherogenic risk indices, such as the atherogenic index plasma (AIP), cardiac risk ratio (CRR), and atherogenic coefficient (AC) in isoproterenol-induced MI rats. In MI rats, NCEE therapy significantly improved the antioxidant system of the heart tissue, as evidenced by the increased levels of GSH and SOD, lower levels of the oxidative stress marker MDA, and significantly decreased HMG-CoA activity. Additionally, electrocardiogram (ECG) signals from rats treated with NCEE resembled those treated with traditional atorvastatin to treat myocardial infarction. This study used H&E staining to show that administering NCEE before treatment reduced cardiac myocyte degeneration in rats with myocardial infarction, increased the presence of intact nuclei, and increased myocardial fiber strength. The potential cardioprotective effect observed in myocardial infarction (MI) rats treated with NCEE can be extrapolated from computational data to be caused by Cinchonain Ib.
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Affiliation(s)
- Raghupathi Niranjan Kumar
- Department of Pharmacology, Santhiram College of Pharmacy, JNTUA, Nandyal 518112, Andhra Pradesh, India; (R.N.K.); (P.G.M.)
| | - Dsnbk Prasanth
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada 520010, Andhra Pradesh, India;
| | - Praisy Gladys Midthuri
- Department of Pharmacology, Santhiram College of Pharmacy, JNTUA, Nandyal 518112, Andhra Pradesh, India; (R.N.K.); (P.G.M.)
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Srikanth Kumar Karumanchi
- Department of Pharmaceutical Chemistry, DKSS Institute of Pharmaceutical Science & Research (for Girls), Swami-Chincholi, Bhigwan 413130, Maharashtra, India;
| | | | - Rahul Nalluri
- Department of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA;
| | - Praveen Kumar Pasala
- Department of Pharmacology, Raghavendra Institute of Pharmaceutical Education and Research, JNTUA, Anantapuramu 515721, Andhra Pradesh, India
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Killari KN, Polimati H, Prasanth DSNBK, Singh G, Panda SP, Vedula GS, Tatipamula VB. Salazinic acid attenuates male sexual dysfunction and testicular oxidative damage in streptozotocin-induced diabetic albino rats. RSC Adv 2023; 13:12991-13005. [PMID: 37124014 PMCID: PMC10132129 DOI: 10.1039/d3ra01542d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/21/2023] [Indexed: 05/02/2023] Open
Abstract
Male sexual dysfunctions such as infertility and impotence are recognized as the consequences of diabetes. Salazinic acid (Sa) is a depsidone found in lichen genera of Lobaria, Parmelia, and Usnea, which has prominent free radical and α-glucosidase inhibitory actions. The present study establishes the beneficial role of salazinic acid (Sa) to combat the deleterious effects of streptozotocin-induced diabetes on the male reproductive system of rats. In a dose-dependent manner, Sa significantly restored the reproductive organs weight, sperm characteristics, and testicular histoarchitecture in diabetic rats. Further, a significant recovery of insulin, follicle-stimulating hormone, luteinizing hormone and testosterone levels in serum was recorded in Sa-treated diabetic rats. The malondialdehyde levels were significantly lowered, and the activities of glutathione, superoxide dismutase, glutathione peroxidase and catalase, markedly elevated in the blood serum, as well as testicular tissue after Sa-supplementation. Sa also suppressed the protein expression levels of tumor necrosis factor-α in serum. The high dose of Sa showed significant improvement in glycemia and testicular protection, similar to sildenafil citrate. Moreover, the docking results showed that both Sa and sildenafil have a high affinity toward the target protein, PDE5 with binding affinity values found to be -9.5 and -9.2 kcal mol-1, respectively. Molecularly, both Sa and sildenafil share similar hydrogen bonding patterns with PDE5. Hence, our study clearly showed the protective role of Sa against diabetic-induced spermatogenic dysfunction in rats, possibly by competing with cGMP to bind to the catalytic domain of PDE5 and thereby controlling the oxidative impairment of testes.
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Affiliation(s)
- Kishore Naidu Killari
- Department of Pharmaceutical Sciences, AU College of Pharmaceutical Sciences, Andhra University Visakhapatnam-530 003 India
| | - Haritha Polimati
- Department of Pharmaceutical Sciences, AU College of Pharmaceutical Sciences, Andhra University Visakhapatnam-530 003 India
| | - D S N B K Prasanth
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences Vijayawada AP 520010 India
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute Jhansi Uttar Pradesh 284003 India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi New Delhi India
| | - Siva Prasad Panda
- Institute Pharmacology Research Division, Institute of Pharmaceutical Research, GLA University 281406 Mathura Uttar Pradesh India
| | - Girija Sastry Vedula
- Department of Pharmaceutical Sciences, AU College of Pharmaceutical Sciences, Andhra University Visakhapatnam-530 003 India
| | - Vinay Bharadwaj Tatipamula
- Center for Molecular Biology, College of Medicine and Pharmacy, Duy Tan University Danang 550000 Vietnam
- Institute of Research and Development, Duy Tan University Da Nang 550000 Vietnam
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In Silico Screening of Plant-Derived Anti-virals from Shorea hemsleyana (King) King ex Foxw Against SARS CoV-2 Main Protease. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00521-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ejeh S, Uzairu A, Shallangwa GA, Abechi SE. Computational insight to design new potential hepatitis C virus NS5B polymerase inhibitors with drug-likeness and pharmacokinetic ADMET parameters predictions. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00373-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Hepatitis C virus (HCV) is considered a worldwide health problem since it affects over 3% of the population and causes 300,000 fatalities per year. Chronic infection causes high morbidity and mortality in patients, leading to liver cirrhosis, hepatocellular carcinoma, fibrosis, liver cancer, and other HCV-related illnesses. Finding novel and better HCV treatments is a top international health goal right now. As a result, the pressing need for new HCV antiviral drugs has fueled research into the structural requirements of NS5B polymerase inhibitors at a molecular basis.
Results
In this study, an in silico technique was applied to study 79 compounds with HCV inhibitory bioactivity, with the best statistical results ($$R^{2}$$
R
2
= 0.7051, $$Q^{2}$$
Q
2
= 0.6455, $$R_{{{\text{pred}}}}^{2}$$
R
pred
2
= 0.6992, $$^{{\text{c}}} R_{{\text{r}}}^{2}$$
c
R
r
2
= 0.6570, SEE = 0.2694).
Conclusions
This QSAR investigation allowed the research team to evaluate the influence of straightforward descriptors, shedding insight into the critical elements that guide the design of innovative effective molecules. Most of the innovative effective molecules exhibited better binding affinity (− 195.6 kcal/mol) than dasabuvir the reference drug (− 171.0 kcal/mol) with the target receptor (hepatitis C virus NS5B RNA polymerase). ADMET prediction disclosed enhanced pharmacokinetic properties with lower MRTD (maximum tolerated dose) of some new derivatives.
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