The emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a long pandemic, with numerous cases and victims worldwide and enormous consequences on social and economic life. Although vaccinations have proceeded and provide a valuable shield against the virus, the approved drugs are limited and it is crucial that further ways to combat infection are developed, that can also act against potential mutations. The main protease (Mpro) of the virus is an appealing target for the development of inhibitors, due to its importance in the viral life cycle and its high conservation among different coronaviruses. Several compounds have shown inhibitory potential against Mpro, both in silico and in vitro, with few of them also having entered clinical trials. These candidates include: known drugs that have been repurposed, molecules specifically designed based on the natural substrate of the protease or on structural moieties that have shown high binding affinity to the protease active site, as well as naturally derived compounds, either isolated or in plant extracts. The aim of this work is to collectively present the results of research regarding Mpro inhibitors to date, focusing on the function of the compounds founded by in silico simulations and further explored by in vitro and in vivo assays. Creating an extended portfolio of promising compounds that may block viral replication by inhibiting Mpro and by understanding involved structure–activity relationships, could provide a basis for the development of effective solutions against SARS-CoV-2 and future related outbreaks. 

https://doi.org/10.1016/j.csbj.2022.03.009

Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds

In this study, we examined aqueous extracts of the edible mushrooms Pleurotus ostreatus (oyster mushroom) and Lentinula edodes (shiitake mushroom). Proteome analysis was conducted using LC-Triple TOF-MS and showed the expression of 753 proteins by Pleurotus ostreatus, and 432 proteins by Lentinula edodes. Bioactive peptides: Rab GDP dissociation inhibitor, superoxide dismutase, thioredoxin reductase, serine proteinase and lectin, were identified in both mushrooms. The extracts also included promising bioactive compounds including phenolics, flavonoids, vitamins and amino acids. The extracts showed promising antiviral activities, with a selectivity index (SI) of 4.5 for Pleurotus ostreatus against adenovirus (Ad7), and a slight activity for Lentinula edodes against herpes simplex-II (HSV-2). The extracts were not cytotoxic to normal human peripheral blood mononuclear cells (PBMCs). On the contrary, they showed moderate cytotoxicity against various cancer cell lines. Additionally, antioxidant activity was assessed using DPPH radical scavenging, ABTS radical cation scavenging and ORAC assays. The two extracts showed potential antioxidant activities, with the maximum activity seen for Pleurotus ostreatus (IC50 µg/mL) = 39.46 ± 1.27 for DPPH; 11.22 ± 1.81 for ABTS; and 21.40 ± 2.20 for ORAC assays. This study encourages the use of these mushrooms in medicine in the light of their low cytotoxicity on normal PBMCs vis a vis their antiviral, antitumor and antioxidant capabilities.

https://www.mdpi.com/1420-3049/26/15/4623/pdf

Proteome Analysis and In Vitro Antiviral, Anticancer and Antioxidant Capacities of the Aqueous Extracts of Lentinula edodes and Pleurotus ostreatus Edible Mushrooms

In this study, we investigated aqueous extracts of three edible mushrooms: Agaricus bisporus (white button mushroom), Pleurotus columbinus (oyster mushroom), and Pleurotus sajor-caju (grey oyster mushroom). The extracts were biochemically characterized for total carbohydrate, phenolic, flavonoid, vitamin, and protein contents besides amino acid analysis. Triple TOF proteome analysis showed 30.1% similarity between proteomes of the two Pleurotus spp. All three extracts showed promising antiviral activities. While Pleurotus columbinus extract showed potent activity against adenovirus (Ad7, selectivity index (SI) = 4.2), Agaricus bisporus showed strong activity against herpes simplex II (HSV-2; SI = 3.7). The extracts showed low cytotoxicity against normal human peripheral blood mononuclear cells (PBMCs) and moderate cytotoxicity against prostate (PC3, DU-145); colorectal (Colo-205); cecum carcinoma (LS-513); liver carcinoma (HepG2); cervical cancer (HeLa); breast adenocarcinoma (MDA-MB-231 and MCF-7) as well as leukemia (CCRF-CEM); acute monocytic leukemia (THP1); acute promyelocytic leukemia (NB4); and lymphoma (U937) cell lines. Antioxidant activity was evaluated using 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging, 2,2'-Azinobis-(3-Ethylbenzthiazolin-6-Sulfonic Acid) ABTS radical cation scavenging, and oxygen radical absorbance capacity (ORAC) assays. The three extracts showed potential antioxidant activities with the maximum activity recorded for Pleurotus columbinus (IC50 µg/mL) = 35.13 ± 3.27 for DPPH, 13.97 ± 4.91 for ABTS, and 29.42 ± 3.21 for ORAC assays.

Antiviral, Cytotoxic, and Antioxidant Activities of Three Edible Agaricomycetes Mushrooms: Pleurotus columbinus, Pleurotus sajor-caju, and Agaricus bisporus.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected billions and has killed millions to date. Studies are being carried out to find therapeutic molecules that can potentially inhibit the replication of SARS-CoV-2. 3-chymotrypsin-like protease (3CL pro) involved in the polyprotein cleavage process is believed to be the key target for viral replication, and hence is an attractive target for the discovery of antiviral molecules. In the present study, we aimed to identify natural phytocompounds from Bridelia retusa as potential inhibitors of SARS-CoV-2 3CL pro (PDB ID: 6M2N) using in silico techniques. Molecular docking studies conducted with three different tools in triplicates revealed that ellagic acid (BR6) and (+)-sesamin (BR13) has better binding affinity than the co-crystal inhibitor “3WL” of 6M2N. BR6 and BR13 were found to have a high LD50 value with good bioavailability. 3WL, BR6, and BR13 bind to the same active binding site and interacted with the HIS41-CYS145 catalytic dyad including other crucial amino acids. Molecular dynamics simulation studies revealed stability of protein–ligand complexes as evidenced from root-mean-square deviations, root-mean-square fluctuations (RMSF), protein secondary structure elements, ligand-RMSF, protein–ligand contacts, ligand torsions, and ligand properties. BR6 (−22.3064 kcal/mol) and BR13 (−19.1274 kcal/mol) showed a low binding free energy value. The Bayesian statistical model revealed BR6 and BR13 as better protease inhibitors than 3WL. Moreover, BR6 and BR13 had already been reported to elicit antiviral activities. Therefore, we conclude that ellagic acid and (+)-sesamin as natural antiviral phytocompounds with inhibitory potential against SARS-CoV-2 3CL pro. 

/pdf/antiviral-phytocompounds-ellagic-acid-and-sesamin-of-27ddqt1g.pdf

Antiviral phytocompounds “ellagic acid” and “(+)-sesamin” of Bridelia retusa identified as potential inhibitors of SARS-CoV-2 3CL pro using extensive molecular docking, molecular dynamics simulation studies, binding free energy calculations, and bioactivity prediction

Abstract The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and M pro , interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed. 

/pdf/small-molecules-in-the-treatment-of-covid-19-313d7e1y.pdf

Small molecules in the treatment of COVID-19

This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the molecular interaction and stability by using docking and molecular dynamics simulations. GC-MS analysis suggested for the isolation of terpenoids compounds as major compounds on methanol extract of pseudostems and rhizomes. Isolation and LC-MS/MS analysis identified 5-hydro-7, 8, 2′-trimethoxyflavanone (9), (E)-hexadecyl-ferulate (1), isocyperol (2), N-isobutyl-(2E,4E)-octadecadienamide (3), and nootkatone (4) from the rhizome extract, as well as from the leaves extract with the absence of 9. Three known steroid compounds, i.e., spinasterone (7), spinasterol (8), and 24-methylcholesta-7-en-3β-on (6), were further identified from the pseudostem extract. Molecular docking showed that steroids compounds 7, 8, and 6 have lower predictive binding energies (MMGBSA) than other metabolites with binding energy of −87.91, −78.11, and −68.80 kcal/mole, respectively. Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). MD simulations showed the complex stability with compound 6 during 100 ns simulation time.

GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe.

Introduction: Human immunodeficiency virus type-1 (HIV-1) that causes acquired immunodeficiency syndrome (AIDS) has become a worldwide health problem today. There are approximately 30 anti-HIV-1 drugs that have been used in the treatment of AIDS. However, effective anti HIV-1 agents with less side affect and high inhibition potency are still in demand. Objective: The objective of this study was to identify the potential compounds from Zingiberaceae plants that might be active as anti-HIV-1 by molecular docking. Materials and Methods: Molecular docking simulation was performed by using AutoDock 4.2 on Linux operation system. Docking protocol was validated by using root mean square deviation (RMSD) value using redocking and cross-docking methods. The reported metabolites from Zingiberaceae plants were docked on HIV-1 protease, integrase, and reverse transcriptase protein enzymes. Results: The docking result showed that the genera of Zingiber, Etlingera, Alpinia, Hedychium, and Boesenbergia have potential metabolites that inhibit HIV protease, integrase, and reverse transcriptase enzymes by possessing lower docking energy than native ligand of amprenavir, raltegravir, and nevirapine. Among the metabolites, noralpindenoside B and alpindenoside A from Alpinia densespicata inhibited protease enzymes with the lowest docking energy of -18.02 and -17.90 kcal/mol, respectively. Meanwhile, panduratin E from Boesenbergia pandurata Roxb. and 5α,8α-epidioxyergosta-6,22-dien-3β-ol from Etlingera elatior showed the lowest docking energy on integrase protein with docking energy of -11.97 and -11.41 kcal/mol, respectively. Pahangensin A from Alpinia pahangensis Ridley showed the lowest docking energy on reverse transcriptase enzyme with docking energy of -13.76 kcal/mol. Conclusion: The docking molecular study has identified the possible potential compounds from Zingiberaceae plants that might be used for anti-HIV-1 treatment. So, this study suggested further isolation and purification of the predicted compounds.

Docking study on anti-HIV-1 activity of secondary metabolites from Zingiberaceae plants

This study aims to determine the content of secondary metabolites and the levels of total secondary metabolites in ethanol extract of Okra (Abelmoschus esculentus L. Moench) fruit with UV-Vis Spectrophotometry method. Okra (Abelmoschus esculentus L. Moench) fruit extract was prepared by maceration method with 96% ethanol. The extract was concentrated using a rotary evaporator that followed by a qualitative test for alkaloids, flavonoids, saponins, and tannins using suitable reagents with the test parameters, while for the qualitative assay using a UV-Vis Spectrophotometry. Qualitative analysis of alkaloids using test parameters of total alkaloids equivalent to quinine, flavonoid using parameter of total flavonoids equivalent to quercetin, saponin using parameters of standard saponins total from the Quillaja Bark, and tannin using test parameters of total tannins equivalent to tannic acid. Qualitative test results indicated that the ethanol extract of Okra fruit tested positive for alkaloids content wich characterized by the orange deposition, flavonoids characterized by the formation of an orange-yellow color, a stable foam for saponins and tannins marked in black. The quantitative analysis resulted alkaloids of 2228.06 mg/gram, flavonoids of 2.79 mg/gram, saponins of 10.03 mg/gram, and tannins of 1973.27 mg/gram.
Keywords: Okra fruit, secondary metabolites, UV- Vis spectrophotometry, qualitative, quantitative.

/pdf/analisis-kualitatif-dan-kuantitatif-metabolit-sekunder-1qexwm8cho.pdf

Analisis Kualitatif dan Kuantitatif Metabolit Sekunder Ekstrak Etanol Buah Okra (Abelmoschus esculentus L. Moench) dengan Metode Spektrofotometri UV-Vis: Qualitative and Quantitative Analysis of Secondary Metabolites in Ethanol Extract of Okra (Abelmoschus esculentus L. Moench) Fruit with UV-Vis Spectrophotometry Method

Ikan sidat (Anguilla marmorata (Q.) Gaimard) memiliki keunggulan gizi atau nutrisi yang tinggi seperti protein, asam lemak, dan vitamin. Penelitian ini bertujuan untuk membandingkan kadar vitamin B (B1, B2, B3, B5, B6, B7, B9, dan B12) pada ikan sidat fase yellow eel dan silver eel asal Sungai Palu Sulawesi Tengah. Metode yang digunakan yaitu purposive sampling berdasarkan pada tempat, ukuran, dan fase ikan. Hasil pengujian vitamin B (B1, B2, B3, B5, B6, dan B9) menggunakan Kromatografi Cair Kinerja Ultra menunjukkan bahwa vitamin B2 fase yellow eel sebesar 0,07 mg/100 g; silver eel sebesar 0,05 mg/100 g; vitamin B3 fase yellow eel sebesar 0,3 mg/100 g; silver eel sebesar 1,16 mg/100 g; dan untuk vitamin B1, B5, B6, dan B9 tidak terdeteksi kadarnya. Sedangkan pengujian vitamin B7 dan B12 menggunakan Kromatografi Cair-Spektrometri Massa menunjukkan bahwa vitamin B7 fase yellow eel sebesar 58,35 µg/100 g; silver eel sebesar 10,61 µg/100 g; vitamin B12 fase yellow eel sebesar 0,52 µg/100 g; dan silver eel sebesar 0,27 µg/100 g. Kesimpulan yaitu vitamin B7 dengan menggunakan Kromatografi Cair-Spektrometri Massa memiliki kadar vitamin tertinggi sebesar 58,35 µg/100 g pada fase yellow eel dan untuk vitamin B3 (Nicotinamide) menggunakan Kromatografi Cair Kinerja Ultra memiliki kadar vitamin terendah sebesar 0,3 mg/100 g pada fase yellow eel.

Studi Perbandingan Kandungan Vitamin B Ikan Sidat (Anguilla marmorata (Q.) Gaimard) Fase Yellow Eel dan Silver Eel Asal Sungai Palu Sulawesi Tengah

Traditional herbal substances are used in alternative diabetes mellitus care programs. This research aimed to determine the secondary metabolite levels of ethanol extract Ocimum basilicum L. leaves, clarify the effect of extracts on blood glucose levels, and histopathological pancreatic tissue Streptozotocin-induced diabetic rats. Phytochemical screening of extracts was carried out qualitatively according to standard methods. UV-Vis Spectrophotometric was the quantitative estimation of alkaloids, flavonoids, saponins, and tannins. The rats were treated with ethanol extract of O. basilicum L. leaves with a dose of 200, 400, and 800 mg/kg bodyweight for 28 days, then calculated with blood levels and histopathology of pancreatic tissue in the group treated and compared to the group of diabetes. Group doses of 400 and 800 mg/kg body weight could significantly reduce blood glucose levels, and according to histological results, can regenerate mouse pancreatic cells. It could conclude that the ethanol extract of O. basilicum L. leaves is a potential source of antidiabetic.

https://rasayanjournal.co.in/admin/php/upload/3109_pdf.pdf

Agustinus Widodo

Papers

GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe.

Docking study on anti-HIV-1 activity of secondary metabolites from Zingiberaceae plants

Studi Perbandingan Kandungan Vitamin B Ikan Sidat (Anguilla marmorata (Q.) Gaimard) Fase Yellow Eel dan Silver Eel Asal Sungai Palu Sulawesi Tengah

QUALITATIVE AND QUANTITATIVE DETERMINATION OF SECONDARY METABOLITES AND ANTIDIABETIC POTENTIAL OF Ocimum basilicum L. LEAVES EXTRACT