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Rosa LS, Argolo CO, Nascimento CM, Pimentel AS. Identifying Substructures That Facilitate Compounds to Penetrate the Blood-Brain Barrier via Passive Transport Using Machine Learning Explainer Models. ACS Chem Neurosci 2024; 15:2144-2159. [PMID: 38723285 PMCID: PMC11157485 DOI: 10.1021/acschemneuro.3c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
The local interpretable model-agnostic explanation (LIME) method was used to interpret two machine learning models of compounds penetrating the blood-brain barrier. The classification models, Random Forest, ExtraTrees, and Deep Residual Network, were trained and validated using the blood-brain barrier penetration dataset, which shows the penetrability of compounds in the blood-brain barrier. LIME was able to create explanations for such penetrability, highlighting the most important substructures of molecules that affect drug penetration in the barrier. The simple and intuitive outputs prove the applicability of this explainable model to interpreting the permeability of compounds across the blood-brain barrier in terms of molecular features. LIME explanations were filtered with a weight equal to or greater than 0.1 to obtain only the most relevant explanations. The results showed several structures that are important for blood-brain barrier penetration. In general, it was found that some compounds with nitrogenous substructures are more likely to permeate the blood-brain barrier. The application of these structural explanations may help the pharmaceutical industry and potential drug synthesis research groups to synthesize active molecules more rationally.
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Affiliation(s)
- Lucca
Caiaffa Santos Rosa
- Departamento de Química, Pontifícia Universidade Católica do
Rio de Janeiro, Rio de
Janeiro, RJ 22453-900, Brazil
| | - Caio Oliveira Argolo
- Departamento de Química, Pontifícia Universidade Católica do
Rio de Janeiro, Rio de
Janeiro, RJ 22453-900, Brazil
| | | | - Andre Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do
Rio de Janeiro, Rio de
Janeiro, RJ 22453-900, Brazil
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2
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Shamsian S, Nabipour I, Mohebbi G, Baghban N, Zare M, Zandi K, Vazirizadeh A, Maryamabadi A, Delattre C. In-vitro and in-silico anti-HSV-1 activity of a marine steroid from the jellyfish Cassiopea andromeda venom. Microb Pathog 2024; 186:106486. [PMID: 38056601 DOI: 10.1016/j.micpath.2023.106486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
In this study, we investigated the potential in vitro anti-HSV-1 activities of the Cassiopea andromeda jellyfish tentacle extract (TE) and its fractions, as well as computational work on the thymidine kinase (TK) inhibitory activity of the identified secondary metabolites. The LD50, secondary metabolite identification, preparative and analytical chromatography, and in silico TK assessment were performed using the Spearman-Karber, GC-MS, silica gel column chromatography, RP-HPLC, LC-MS, and docking methods, respectively. The antiviral activity of TE and the two purified compounds Ca2 and Ca7 against HSV-1 in Vero cells was evaluated by MTT and RT-PCR assays. The LD50 (IV, mouse) values of TE, Ca2, and Ca7 were 104.0 ± 4, 5120 ± 14, and 197.0 ± 7 (μg/kg), respectively. They exhibited extremely effective antiviral activity against HSV-1. The CC50 and MNTD of TE, Ca2, and Ca7 were (125, 62.5), (25, 12.5), and (50, 3.125) μg/ml, respectively. GC-MS analysis of the tentacle extract revealed seven structurally distinct chemical compositions. Four of the seven compounds had a steroid structure. According to the docking results, all compounds showed binding affinity to the active sites of both thymidine kinase chains. Among them, the steroid compound Pregn-5-ene-3,11-dione, 17,20:20,21 bis [methylenebis(oxy)]-, cyclic 3-(1,2-ethane diyl acetal) (Ca2) exhibited the highest affinity for both enzyme chains, surpassing that of standard acyclovir. In silico data confirmed the experimental results. We conclude that the oxosteroid Ca2 may act as a potent agent against HSV-1.
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Affiliation(s)
- Shakib Shamsian
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Gholamhossein Mohebbi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Neda Baghban
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Masoud Zare
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Keivan Zandi
- Tropical Infectious Diseases Research and Education Center (TIDREC), University of Malaya, Kuala Lumpur, Malaysia.
| | - Amir Vazirizadeh
- Department of Marine Biotechnology, The Persian Gulf Research and Studies Center, The Persian Gulf University, Bushehr, Iran.
| | - Ammar Maryamabadi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Cédric Delattre
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, F-63000, Clermont-Ferrand, France; Institut Universitaire de France (IUF), 1 Rue Descartes, 7500, Paris, France.
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3
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor Ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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Hafez MSMAE, Rashedy SH, Abdelmotilib NM, El-Hassayeb HEA, Cotas J, Pereira L. Fillet Fish Fortified with Algal Extracts of Codium tomentosum and Actinotrichia fragilis, as a Potential Antibacterial and Antioxidant Food Supplement. Mar Drugs 2022; 20:md20120785. [PMID: 36547932 PMCID: PMC9781850 DOI: 10.3390/md20120785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
With respect to the potential natural resources in the marine environment, marine macroalgae or seaweeds are recognized to have health impacts. Two marine algae that are found in the Red Sea, Codium tomentosum (Green algae) and Actinotrichia fragilis (Red algae), were collected. Antibacterial and antioxidant activities of aqueous extracts of these algae were evaluated in vitro. Polyphenols from the extracts were determined using HPLC. Fillet fish was fortified with these algal extracts in an attempt to improve its nutritional value, and sensory evaluation was performed. The antibacterial effect of C. tomentosum extract was found to be superior to that of A. fragilis extract. Total phenolic contents of C. tomentosum and A. fragilis aqueous extract were 32.28 ± 1.63 mg/g and 19.96 ± 1.28 mg/g, respectively, while total flavonoid contents were 4.54 ± 1.48 mg/g and 3.86 ± 1.02 mg/g, respectively. Extract of C. tomentosum demonstrates the highest antioxidant activity, with an IC50 value of 75.32 ± 0.07 μg/mL. The IC50 of L-ascorbic acid as a positive control was 22.71 ± 0.03 μg/mL. The IC50 values for inhibiting proliferation on normal PBMC cells were 33.7 ± 1.02 µg/mL and 51.0 ± 1.14 µg/mL for C. tomentosum and A. fragilis, respectively. The results indicated that both algal aqueous extracts were safe, with low toxicity to normal cells. Interestingly, fillet fish fortified with C. tomentosum extract demonstrated the greatest overall acceptance score. These findings highlight the potential of these seaweed species for cultivation as a sustainable and safe source of therapeutic compounds for treating human and fish diseases, as well as effective food supplements and preservatives instead of chemical ones after performing in vivo assays.
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Affiliation(s)
- Mohamed S. M. Abd El Hafez
- National Institute of Oceanography and Fisheries, NIOF, Cairo 11516, Egypt
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industries Development Center (PFIDC), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Egypt
- Correspondence: (M.S.M.A.E.H.); (L.P.)
| | - Sarah H. Rashedy
- National Institute of Oceanography and Fisheries, NIOF, Cairo 11516, Egypt
| | - Neveen M. Abdelmotilib
- Department of Food Technology, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-CITY), New Borg El-Arab City 21934, Egypt
| | | | - João Cotas
- MARE—Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Leonel Pereira
- MARE—Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Correspondence: (M.S.M.A.E.H.); (L.P.)
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Sen S, Singh B, Biswas G. Corticosteroids: A boon or bane for COVID-19 patients? Steroids 2022; 188:109102. [PMID: 36029810 PMCID: PMC9400384 DOI: 10.1016/j.steroids.2022.109102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 07/29/2022] [Accepted: 08/19/2022] [Indexed: 01/11/2023]
Abstract
Several drugs and antibodies have been repurposed to treat COVID-19. Since the outcome of the drugs and antibodies clinical studies have been mostly inconclusive or with lesser effects, therefore the need for alternative treatments has become unavoidable. However, corticosteroids, which have a history of therapeutic efficacy against coronaviruses (SARS and MERS), might emerge into one of the pandemic's heroic characters. Corticosteroids serve an immunomodulatory function in the post-viral hyper-inflammatory condition (the cytokine storm, or release syndrome), suppressing the excessive immunological response and preventing multi-organ failure and death. Therefore, corticosteroids have been used to treat COVID-19 patients for more than last two years. According to recent clinical trials and the results of observational studies, corticosteroids can be administered to patients with severe and critical COVID-19 symptoms with a favorable risk-benefit ratio. Corticosteroids like Hydrocortisone, dexamethasone, Prednisolone and Methylprednisolone has been reported to be effective against SARS-CoV-2 virus in comparison to that of non-steroid drugs, by using non-genomic and genomic effects to prevent and reduce inflammation in tissues and the circulation. Clinical trials also show that inhaled budesonide (a synthetic corticosteroid) increases time to recovery and has the potential to reduce hospitalizations or fatalities in persons with COVID-19. There is also a brief overview of the industrial preparation of common glucocorticoids.
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Affiliation(s)
- Subhadeep Sen
- Department of Chemistry, Cooch Behar Panchanan Barma University, Panchanan Nagar, Cooch Behar 736101, West Bengal, India
| | - Bhagat Singh
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Goutam Biswas
- Department of Chemistry, Cooch Behar Panchanan Barma University, Panchanan Nagar, Cooch Behar 736101, West Bengal, India.
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Abdelkarem FM, Nafady AM, Allam AE, Mostafa MAH, Al Haidari RA, Hassan HA, Zaki MEA, Assaf HK, Kamel MR, Zidan SAH, Sayed AM, Shimizu K. A Comprehensive In Silico Study of New Metabolites from Heteroxenia fuscescens with SARS-CoV-2 Inhibitory Activity. Molecules 2022; 27:molecules27217369. [PMID: 36364194 PMCID: PMC9657797 DOI: 10.3390/molecules27217369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 12/02/2022] Open
Abstract
Chemical investigation of the total extract of the Egyptian soft coral Heteroxenia fuscescens, led to the isolation of eight compounds, including two new metabolites, sesquiterpene fusceterpene A (1) and a sterol fuscesterol A (4), along with six known compounds. The structures of 1–8 were elucidated via intensive studies of their 1D, 2D-NMR, and HR-MS analyses, as well as a comparison of their spectral data with those mentioned in the literature. Subsequent comprehensive in-silico-based investigations against almost all viral proteins, including those of the new variants, e.g., Omicron, revealed the most probable target for these isolated compounds, which was found to be Mpro. Additionally, the dynamic modes of interaction of the putatively active compounds were highlighted, depending on 50-ns-long MDS. In conclusion, the structural information provided in the current investigation highlights the antiviral potential of H. fuscescens metabolites with 3β,5α,6β-trihydroxy steroids with different nuclei against SARS-CoV-2, including newly widespread variants.
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Affiliation(s)
- Fahd M. Abdelkarem
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Alaa M. Nafady
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Ahmed E. Allam
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
- Correspondence: (A.E.A.); (M.E.A.Z.)
| | - Mahmoud A. H. Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al Madinah Al Munawarah 41477, Saudi Arabia
| | - Rwaida A. Al Haidari
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al Madinah Al Munawarah 41477, Saudi Arabia
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Correspondence: (A.E.A.); (M.E.A.Z.)
| | - Hamdy K. Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Mohamed R. Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Sabry A. H. Zidan
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
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Ramalingam A, Kuppusamy M, Sambandam S, Medimagh M, Oyeneyin OE, Shanmugasundaram A, Issaoui N, Ojo ND. Synthesis, spectroscopic, topological, hirshfeld surface analysis, and anti-covid-19 molecular docking investigation of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate. Heliyon 2022; 8:e10831. [PMID: 36211997 PMCID: PMC9526874 DOI: 10.1016/j.heliyon.2022.e10831] [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: 08/18/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
Isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate (IDPC) was synthesized and characterized via spectroscopic (FT-IR and NMR) techniques. Hirshfeld surface and topological analyses were conducted to study structural and molecular properties. The energy gap (Eg), frontier orbital energies (EHOMO, ELUMO) and reactivity parameters (like chemical hardness and global hardness) were calculated using density functional theory with B3LYP/6-311++G (d,p) level of theory. Molecular docking of IDPC at the active sites of SARS-COVID receptors was investigated. IDPC molecule crystallized in the centrosymmetric triclinic ( P 1 ¯ ) space group. The topological and Hirshfeld surface analysis revealed that covalent, non-covalent and intermolecular H-bonding interactions, and electron delocalization exist in the molecular framework. Higher binding score (-6.966 kcal/mol) of IDPC at the active site of SARS-COVID main protease compared to other proteases suggests that IDPC has the potential of blocking polyprotein maturation. H-bonding and π-cationic and interactions of the phenyl ring and carbonyl oxygen of the ligand indicate the effective inhibiting potential of the compound against the virus.
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Affiliation(s)
- Arulraj Ramalingam
- Department of Electrical and Computer Engineering, National University of Singapore, 117583, Singapore
| | - Murugavel Kuppusamy
- PG & Research Department of Chemistry, Government Arts College, Chidambaram, Tamil Nadu, India
| | - Sivakumar Sambandam
- Research and Development Centre, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Mouna Medimagh
- University of Monastir, Faculty of Sciences, Laboratory of Quantum and Statistical Physics (LR18ES18), Monastir, 5079, Tunisia
| | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | | | - Noureddine Issaoui
- University of Monastir, Faculty of Sciences, Laboratory of Quantum and Statistical Physics (LR18ES18), Monastir, 5079, Tunisia
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