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Arivuselvam R, Dera AA, Parween Ali S, Alraey Y, Saif A, Hani U, Arumugam Ramakrishnan S, Azeeze MSTA, Rajeshkumar R, Susil A, Harindranath H, Kumar BRP. Isolation, Identification, and Antibacterial Properties of Prodigiosin, a Bioactive Product Produced by a New Serratia marcescens JSSCPM1 Strain: Exploring the Biosynthetic Gene Clusters of Serratia Species for Biological Applications. Antibiotics (Basel) 2023; 12:1466. [PMID: 37760761 PMCID: PMC10526024 DOI: 10.3390/antibiotics12091466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Prodigiosin pigment has high medicinal value, so exploring this compound is a top priority. This report presents a prodigiosin bioactive compound isolated from Serratia marcescens JSSCPM1, a new strain. The purification process of this compound involves the application of different chromatographic methods, including UV-visible spectroscopy, high-performance liquid chromatography (HPLC), and liquid chromatography-mass spectrometry (LC/MS). Subsequent analysis was performed using nuclear magnetic resonance (NMR) to achieve a deeper understanding of the compound's structure. Finally, through a comprehensive review of the existing literature, the structural composition of the isolated bioactive compound was found to correspond to that of the well-known compound prodigiosin. The isolated prodigiosin compound was screened for antibacterial activity against both Gram-positive and Gram-negative bacteria. The compound inhibited the growth of Gram-negative bacterial strains compared with Gram-positive bacterial strains. It showed a maximum minimum inhibitory concentration against Escherichia coli NCIM 2065 at a 15.9 ± 0.31 μg/mL concentration. The potential binding capabilities between prodigiosin and the OmpF porin proteins (4GCS, 4GCP, and 4GCQ) were determined using in silico studies, which are generally the primary targets of different antibiotics. Comparative molecular docking analysis indicated that prodigiosin exhibits a good binding affinity toward these selected drug targets.
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Affiliation(s)
- Rajaguru Arivuselvam
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India
| | - Ayed A. Dera
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Syed Parween Ali
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Yasser Alraey
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia;
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Guraiger, Abha 62529, Saudi Arabia;
| | - Sivaa Arumugam Ramakrishnan
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India
| | | | - Raman Rajeshkumar
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
| | - Aishwarya Susil
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
| | - Haritha Harindranath
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
| | - B. R. Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
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Srivathsa AV, Sadashivappa NM, Hegde AK, Radha S, Mahesh AR, Ammunje DN, Sen D, Theivendren P, Govindaraj S, Kunjiappan S, Pavadai P. A Review on Artificial Intelligence Approaches and Rational Approaches in Drug Discovery. Curr Pharm Des 2023; 29:1180-1192. [PMID: 37132148 DOI: 10.2174/1381612829666230428110542] [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: 11/30/2022] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 05/04/2023]
Abstract
Artificial intelligence (AI) speeds up the drug development process and reduces its time, as well as the cost which is of enormous importance in outbreaks such as COVID-19. It uses a set of machine learning algorithms that collects the available data from resources, categorises, processes and develops novel learning methodologies. Virtual screening is a successful application of AI, which is used in screening huge drug-like databases and filtering to a small number of compounds. The brain's thinking of AI is its neural networking which uses techniques such as Convoluted Neural Network (CNN), Recursive Neural Network (RNN) or Generative Adversial Neural Network (GANN). The application ranges from small molecule drug discovery to the development of vaccines. In the present review article, we discussed various techniques of drug design, structure and ligand-based, pharmacokinetics and toxicity prediction using AI. The rapid phase of discovery is the need of the hour and AI is a targeted approach to achieve this.
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Affiliation(s)
- Anjana Vidya Srivathsa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Nandini Markuli Sadashivappa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Apeksha Krishnamurthy Hegde
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Srimathi Radha
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, Faculty of Medicine and Health Sciences, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu, 603203, India
| | - Agasa Ramu Mahesh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Damodar Nayak Ammunje
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Debanjan Sen
- Department of Pharmaceutical Chemistry, BCDA College of Pharmacy & Technology, Hridaypur, Kolkata, 700127, West Bengal, India
| | - Panneerselvam Theivendren
- Department of Pharmaceutical Chemistry, Swamy Vivekanandha College of Pharmacy, Elayampalayam, Tiruchengode, 637205, India
| | - Saravanan Govindaraj
- Department of Pharmaceutical Chemistry, MNR College of Pharmacy, Fasalwadi, Sangareddy, 502 001, India
| | - Selvaraj Kunjiappan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
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Gallo K, Goede A, Preissner R, Gohlke BO. SuperPred 3.0: drug classification and target prediction-a machine learning approach. Nucleic Acids Res 2022; 50:W726-W731. [PMID: 35524552 PMCID: PMC9252837 DOI: 10.1093/nar/gkac297] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 11/21/2022] Open
Abstract
Since the last published update in 2014, the SuperPred webserver has been continuously developed to offer state-of-the-art models for drug classification according to ATC classes and target prediction. For the first time, a thoroughly filtered ATC dataset, that is suitable for accurate predictions, is provided along with detailed information on the achieved predictions. This aims to overcome the challenges in comparing different published prediction methods, since performance can vary greatly depending on the training dataset used. Additionally, both ATC and target prediction have been reworked and are now based on machine learning models instead of overall structural similarity, stressing the importance of functional groups for the mechanism of action of small molecule substances. Additionally, the dataset for the target prediction has been extensively filtered and is no longer only based on confirmed binders but also includes non-binding substances to reduce false positives. Using these methods, accuracy for the ATC prediction could be increased by almost 5% to 80.5% compared to the previous version, and additionally the scoring function now offers values which are easily assessable at first glance. SuperPred 3.0 is publicly available without the need for registration at: https://prediction.charite.de/index.php.
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Affiliation(s)
- Kathleen Gallo
- Charité - Universitätsmedizin Berlin, Institute of Physiology and Science IT, Corporate Member of Freie Universität Berlin, Berlin Institute of Health, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Andrean Goede
- Charité - Universitätsmedizin Berlin, Institute of Physiology and Science IT, Corporate Member of Freie Universität Berlin, Berlin Institute of Health, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Robert Preissner
- Charité - Universitätsmedizin Berlin, Institute of Physiology and Science IT, Corporate Member of Freie Universität Berlin, Berlin Institute of Health, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Bjoern-Oliver Gohlke
- Charité - Universitätsmedizin Berlin, Institute of Physiology and Science IT, Corporate Member of Freie Universität Berlin, Berlin Institute of Health, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
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Farghaly TA, Alsaedi AMR, Alenazi NA, Harras MF. Anti-viral activity of thiazole derivatives: an updated patent review. Expert Opin Ther Pat 2022; 32:791-815. [DOI: 10.1080/13543776.2022.2067477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Thoraya A. Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Amani M. R. Alsaedi
- Department of Chemistry, Collage of Science, Taif University, Taif 21944, Saudi Arabia
| | - Noof A. Alenazi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Marwa F. Harras
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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Drummondin E and Flinderole B are potential inhibitors of RNA-dependent RNA polymerase of SARS-CoV-2: an in silico study. BIOTECHNOLOGIA 2022; 103:53-70. [PMID: 36605381 PMCID: PMC9642944 DOI: 10.5114/bta.2022.113915] [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: 07/12/2021] [Revised: 10/03/2021] [Accepted: 01/03/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected 235.6 million people worldwide. In the present study, RNA-dependent RNA polymerase (RdRp) (PDB Id: 6M71) of SARS-CoV-2, an essential enzyme needed for subgenomic replication and amplification of RNA, was selected. Similar to other RdRps, it is a conserved protein and a popular target for antiviral drug therapy. Based on a computational approach, potential RdRp inhibitors were identified. The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of selected molecules were determined using computation tools. The potential inhibitors were docked to the RdRp and later confirmed by Molecular Dynamics (MD) using the "Flare" module of Cresset software. Drummondin E and Flinderole B had higher drug similarity scores among the compounds selected in this study. Both these compounds are noncarcinogenic, nonirritant, nontumorigenic, and nonmutagenic. Molecular docking studies showed that both compounds can bind to RdRp. The best ligand interaction patterns were validated by MD using the "Flare" module. MD was performed for the period of 100 ns with the time step of 1 fs. The simulation results suggest that Thr-680, Arg-624, Lys-676, and Val-557 are key interacting partners in the Drummondin E-RdRp complex, while Asp-618, Asp-760, Asp-623, Arg-624, and Asp-761 are the interacting partners in the Flinderole B-RdRp complex. Based on the in silico drug-likeness score; ADMET properties; and molecular simulation result, we surmise that Flinderole B and Drummondin E could impede SARS-CoV-2 genome replication and transcription by targeting the RdRp protein.
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Riyaphan J, Pham DC, Leong MK, Weng CF. In Silico Approaches to Identify Polyphenol Compounds as α-Glucosidase and α-Amylase Inhibitors against Type-II Diabetes. Biomolecules 2021; 11:1877. [PMID: 34944521 PMCID: PMC8699780 DOI: 10.3390/biom11121877] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 01/01/2023] Open
Abstract
Type-II diabetes mellitus (T2DM) results from a combination of genetic and lifestyle factors, and the prevalence of T2DM is increasing worldwide. Clinically, both α-glucosidase and α-amylase enzymes inhibitors can suppress peaks of postprandial glucose with surplus adverse effects, leading to efforts devoted to urgently seeking new anti-diabetes drugs from natural sources for delayed starch digestion. This review attempts to explore 10 families e.g., Bignoniaceae, Ericaceae, Dryopteridaceae, Campanulaceae, Geraniaceae, Euphorbiaceae, Rubiaceae, Acanthaceae, Rutaceae, and Moraceae as medicinal plants, and folk and herb medicines for lowering blood glucose level, or alternative anti-diabetic natural products. Many natural products have been studied in silico, in vitro, and in vivo assays to restrain hyperglycemia. In addition, natural products, and particularly polyphenols, possess diverse structures for exploring them as inhibitors of α-glucosidase and α-amylase. Interestingly, an in silico discovery approach using natural compounds via virtual screening could directly target α-glucosidase and α-amylase enzymes through Monte Carto molecular modeling. Autodock, MOE-Dock, Biovia Discovery Studio, PyMOL, and Accelrys have been used to discover new candidates as inhibitors or activators. While docking score, binding energy (Kcal/mol), the number of hydrogen bonds, or interactions with critical amino acid residues have been taken into concerning the reliability of software for validation of enzymatic analysis, in vitro cell assay and in vivo animal tests are required to obtain leads, hits, and candidates in drug discovery and development.
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Affiliation(s)
| | - Dinh-Chuong Pham
- Biomaterials and Nanotechnology Research Group, Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam;
| | - Max K. Leong
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan
| | - Ching-Feng Weng
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, China
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Kaur M, Yardley V, Wang K, Masania J, Arroo RRJ, Turner DB, Li M. Artemisinin Cocrystals for Bioavailability Enhancement. Part 2: In Vivo Bioavailability and Physiologically Based Pharmacokinetic Modeling. Mol Pharm 2021; 18:4272-4289. [PMID: 34748332 DOI: 10.1021/acs.molpharmaceut.1c00385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the evaluation and prediction of the pharmacokinetic (PK) performance of artemisinin (ART) cocrystal formulations, that is, 1:1 artemisinin/orcinol (ART-ORC) and 2:1 artemisinin/resorcinol (ART2-RES), using in vivo murine animal and physiologically based pharmacokinetic (PBPK) models. The efficacy of the ART cocrystal formulations along with the parent drug ART was tested in mice infected with Plasmodium berghei. When given at the same dose, the ART cocrystal formulation showed a significant reduction in parasitaemia at day 4 after infection compared to ART alone. PK parameters including Cmax (maximum plasma concentration), Tmax (time to Cmax), and AUC (area under the curve) were obtained by determining drug concentrations in the plasma using liquid chromatography-high-resolution mass spectrometry (LC-HRMS), showing enhanced ART levels after dosage with the cocrystal formulations. The dose-response tests revealed that a significantly lower dose of the ART cocrystals in the formulation was required to achieve a similar therapeutic effect as ART alone. A PBPK model was developed using a PBPK mouse simulator to accurately predict the in vivo behavior of the cocrystal formulations by combining in vitro dissolution profiles with the properties of the parent drug ART. The study illustrated that information from classical in vitro and in vivo experimental investigations of the parent drug of ART formulations can be coupled with PBPK modeling to predict the PK parameters of an ART cocrystal formulation in an efficient manner. Therefore, the proposed modeling strategy could be used to establish in vitro and in vivo correlations for different cocrystals intended to improve dissolution properties and to support clinical candidate selection, contributing to the assessment of cocrystal developability and formulation development.
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Affiliation(s)
- Manreet Kaur
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
| | - Vanessa Yardley
- Department of Infection & Immunity, Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, U.K
| | - Ke Wang
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
| | - Jinit Masania
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
| | - Randolph R J Arroo
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
| | - David B Turner
- Certara UK Limited, Simcyp Division, Sheffield S1 2BJ, U.K
| | - Mingzhong Li
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
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Repurposing of the ALK Inhibitor Crizotinib for Acute Leukemia and Multiple Myeloma Cells. Pharmaceuticals (Basel) 2021; 14:ph14111126. [PMID: 34832908 PMCID: PMC8617756 DOI: 10.3390/ph14111126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
Crizotinib was a first generation of ALK tyrosine kinase inhibitor approved for the treatment of ALK-positive non-small-cell lung carcinoma (NSCLC) patients. COMPARE and cluster analyses of transcriptomic data of the NCI cell line panel indicated that genes with different cellular functions regulated the sensitivity or resistance of cancer cells to crizotinib. Transcription factor binding motif analyses in gene promoters divulged two transcription factors possibly regulating the expression of these genes, i.e., RXRA and GATA1, which are important for leukemia and erythroid development, respectively. COMPARE analyses also implied that cell lines of various cancer types displayed varying degrees of sensitivity to crizotinib. Unexpectedly, leukemia but not lung cancer cells were the most sensitive cells among the different types of NCI cancer cell lines. Re-examining this result in another panel of cell lines indeed revealed that crizotinib exhibited potent cytotoxicity towards acute myeloid leukemia and multiple myeloma cells. P-glycoprotein-overexpressing CEM/ADR5000 leukemia cells were cross-resistant to crizotinib. NCI-H929 multiple myeloma cells were the most sensitive cells. Hence, we evaluated the mode of action of crizotinib on these cells. Although crizotinib is a TKI, it showed highest correlation rates with DNA topoisomerase II inhibitors and tubulin inhibitors. The altered gene expression profiles after crizotinib treatment predicted several networks, where TOP2A and genes related to cell cycle were downregulated. Cell cycle analyses showed that cells incubated with crizotinib for 24 h accumulated in the G2M phase. Crizotinib also increased the number of p-H3(Ser10)-positive NCI-H929 cells illustrating crizotinib's ability to prevent mitotic exit. However, cells accumulated in the sub-G0G1 fraction with longer incubation periods, indicating apoptosis induction. Additionally, crizotinib disassembled the tubulin network of U2OS cells expressing an α-tubulin-GFP fusion protein, preventing migration of cancer cells. This result was verified by in vitro tubulin polymerization assays. In silico molecular docking also revealed a strong binding affinity of crizotinib to the colchicine and Vinca alkaloid binding sites. Taken together, these results demonstrate that crizotinib destabilized microtubules. Additionally, the decatenation assay showed that crizotinib partwise inhibited the catalytic activity of DNA topoisomerase II. In conclusion, crizotinib exerted kinase-independent cytotoxic effects through the dual inhibition of tubulin polymerization and topoisomerase II and might be used to treat not only NSCLC but also multiple myeloma.
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Ali SI, Sheikh WM, Rather MA, Venkatesalu V, Muzamil Bashir S, Nabi SU. Medicinal plants: Treasure for antiviral drug discovery. Phytother Res 2021; 35:3447-3483. [PMID: 33590931 PMCID: PMC8013762 DOI: 10.1002/ptr.7039] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022]
Abstract
The pandemic of viral diseases like novel coronavirus (2019-nCoV) prompted the scientific world to examine antiviral bioactive compounds rather than nucleic acid analogous, protease inhibitors, or other toxic synthetic molecules. The emerging viral infections significantly associated with 2019-nCoV have challenged humanity's survival. Further, there is a constant emergence of new resistant viral strains that demand novel antiviral agents with fewer side effects and cell toxicity. Despite significant progress made in immunization and regenerative medicine, numerous viruses still lack prophylactic vaccines and specific antiviral treatments that are so often influenced by the generation of viral escape mutants. Of importance, medicinal herbs offer a wide variety of therapeutic antiviral chemotypes that can inhibit viral replication by preventing viral adsorption, adhering to cell receptors, inhibiting virus penetration in the host cell, and competing for pathways of activation of intracellular signals. The present review will comprehensively summarize the promising antiviral activities of medicinal plants and their bioactive molecules. Furthermore, it will elucidate their mechanism of action and possible implications in the treatment/prevention of viral diseases even when their mechanism of action is not fully understood, which could serve as the base for the future development of novel or complementary antiviral treatments.
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Affiliation(s)
- Sofi Imtiyaz Ali
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Wajid Mohammad Sheikh
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Muzafar Ahmad Rather
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | | | - Showkeen Muzamil Bashir
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Showkat Ul Nabi
- Large Animal Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
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Gallo K, Goede A, Eckert A, Moahamed B, Preissner R, Gohlke BO. PROMISCUOUS 2.0: a resource for drug-repositioning. Nucleic Acids Res 2021; 49:D1373-D1380. [PMID: 33196798 PMCID: PMC7779026 DOI: 10.1093/nar/gkaa1061] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 01/21/2023] Open
Abstract
The development of new drugs for diseases is a time-consuming, costly and risky process. In recent years, many drugs could be approved for other indications. This repurposing process allows to effectively reduce development costs, time and, ultimately, save patients’ lives. During the ongoing COVID-19 pandemic, drug repositioning has gained widespread attention as a fast opportunity to find potential treatments against the newly emerging disease. In order to expand this field to researchers with varying levels of experience, we made an effort to open it to all users (meaning novices as well as experts in cheminformatics) by significantly improving the entry-level user experience. The browsing functionality can be used as a global entry point to collect further information with regards to small molecules (∼1 million), side-effects (∼110 000) or drug-target interactions (∼3 million). The drug-repositioning tab for small molecules will also suggest possible drug-repositioning opportunities to the user by using structural similarity measurements for small molecules using two different approaches. Additionally, using information from the Promiscuous 2.0 Database, lists of candidate drugs for given indications were precomputed, including a section dedicated to potential treatments for COVID-19. All the information is interconnected by a dynamic network-based visualization to identify new indications for available compounds. Promiscuous 2.0 is unique in its functionality and is publicly available at http://bioinformatics.charite.de/promiscuous2.
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Affiliation(s)
- Kathleen Gallo
- Charité Universitaetsmedizin Berlin, Institute of Physiology, Structural Bioinformatics Group, Berlin 10117, Germany
| | - Andrean Goede
- Charité Universitaetsmedizin Berlin, Institute of Physiology, Structural Bioinformatics Group, Berlin 10117, Germany
| | - Andreas Eckert
- Charité Universitaetsmedizin Berlin, Department of Information Technology, Science IT, Berlin 10117, Germany
| | - Barbara Moahamed
- Charité Universitaetsmedizin Berlin, Department of Information Technology, Science IT, Berlin 10117, Germany
| | - Robert Preissner
- Charité Universitaetsmedizin Berlin, Institute of Physiology, Structural Bioinformatics Group, Berlin 10117, Germany.,Charité Universitaetsmedizin Berlin, Department of Information Technology, Science IT, Berlin 10117, Germany
| | - Björn-Oliver Gohlke
- Charité Universitaetsmedizin Berlin, Department of Information Technology, Science IT, Berlin 10117, Germany
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Verma AK, Aggarwal R. Repurposing potential of FDA-approved and investigational drugs for COVID-19 targeting SARS-CoV-2 spike and main protease and validation by machine learning algorithm. Chem Biol Drug Des 2020; 97:836-853. [PMID: 33289334 DOI: 10.1111/cbdd.13812] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/15/2020] [Accepted: 11/29/2020] [Indexed: 12/15/2022]
Abstract
The present study aimed to assess the repurposing potential of existing antiviral drug candidates (FDA-approved and investigational) against SARS-CoV-2 target proteins that facilitates viral entry and replication into the host body. To evaluate molecular affinities between antiviral drug candidates and SARS-CoV-2 associated target proteins such as spike protein (S) and main protease (Mpro ), a molecular interaction simulation was performed by docking software (MVD) and subsequently the applicability score was calculated by machine learning algorithm. Furthermore, the STITCH algorithm was used to predict the pharmacology network involving multiple pathways of active drug candidate(s). Pharmacophore features of active drug(s) molecule was also determined to predict structure-activity relationship (SAR). The molecular interaction analysis showed that cordycepin has strong binding affinities with S protein (-180) and Mpro proteins (-205) which were relatively highest among other drug candidates used. Interestingly, compounds with low IC50 showed high binding energy. Furthermore, machine learning algorithm also revealed high applicability scores (0.42-0.47) of cordycepin. It is worth mentioning that the pharmacology network depicted the involvement of cordycepin in different pathways associated with bacterial and viral diseases including tuberculosis, hepatitis B, influenza A, viral myocarditis, and herpes simplex infection. The embedded pharmacophore features with cordycepin also suggested strong SAR. Cordycepin's anti-SARS-CoV-2 activity indicated 65% (E-gene) and 42% (N-gene) viral replication inhibition after 48h of treatment. Since, cordycepin has both preclinical and clinical evidences on antiviral activity, in addition the present findings further validate and suggest repurposing potential of cordycepin against COVID-19.
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Affiliation(s)
- Akalesh Kumar Verma
- Cell and Biochemical Technology Laboratory, Department of Zoology, Cotton University, Guwahati, India
| | - Rohit Aggarwal
- Cosmic Cordycep Farms, Badarpur Said Tehsil Tigaon, Faridabad, Haryana, India
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12
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An Integrated In Silico and In Vivo Approach to Identify Protective Effects of Palonosetron in Cisplatin-Induced Nephrotoxicity. Pharmaceuticals (Basel) 2020; 13:ph13120480. [PMID: 33419241 PMCID: PMC7766590 DOI: 10.3390/ph13120480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
Cisplatin is widely used to treat various types of cancers, but it is often limited by nephrotoxicity. Here, we employed an integrated in silico and in vivo approach to identify potential treatments for cisplatin-induced nephrotoxicity (CIN). Using publicly available mouse kidney and human kidney organoid transcriptome datasets, we first identified a 208-gene expression signature for CIN and then used the bioinformatics database Cmap and Lincs Unified Environment (CLUE) to identify drugs expected to counter the expression signature for CIN. We also searched the adverse event database, Food and Drug Administration. Adverse Event Reporting System (FAERS), to identify drugs that reduce the reporting odds ratio of developing cisplatin-induced acute kidney injury. Palonosetron, a serotonin type 3 receptor (5-hydroxytryptamine receptor 3 (5-HT3R)) antagonist, was identified by both CLUE and FAERS analyses. Notably, clinical data from 103 patients treated with cisplatin for head and neck cancer revealed that palonosetron was superior to ramosetron in suppressing cisplatin-induced increases in serum creatinine and blood urea nitrogen levels. Moreover, palonosetron significantly increased the survival rate of zebrafish exposed to cisplatin but not to other 5-HT3R antagonists. These results not only suggest that palonosetron can suppress CIN but also support the use of in silico and in vivo approaches in drug repositioning studies.
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13
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Low ZY, Farouk IA, Lal SK. Drug Repositioning: New Approaches and Future Prospects for Life-Debilitating Diseases and the COVID-19 Pandemic Outbreak. Viruses 2020; 12:E1058. [PMID: 32972027 PMCID: PMC7551028 DOI: 10.3390/v12091058] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/02/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
Traditionally, drug discovery utilises a de novo design approach, which requires high cost and many years of drug development before it reaches the market. Novel drug development does not always account for orphan diseases, which have low demand and hence low-profit margins for drug developers. Recently, drug repositioning has gained recognition as an alternative approach that explores new avenues for pre-existing commercially approved or rejected drugs to treat diseases aside from the intended ones. Drug repositioning results in lower overall developmental expenses and risk assessments, as the efficacy and safety of the original drug have already been well accessed and approved by regulatory authorities. The greatest advantage of drug repositioning is that it breathes new life into the novel, rare, orphan, and resistant diseases, such as Cushing's syndrome, HIV infection, and pandemic outbreaks such as COVID-19. Repositioning existing drugs such as Hydroxychloroquine, Remdesivir, Ivermectin and Baricitinib shows good potential for COVID-19 treatment. This can crucially aid in resolving outbreaks in urgent times of need. This review discusses the past success in drug repositioning, the current technological advancement in the field, drug repositioning for personalised medicine and the ongoing research on newly emerging drugs under consideration for the COVID-19 treatment.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
| | - Isra Ahmad Farouk
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
| | - Sunil Kumar Lal
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia
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14
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Dubey KK, Indu, Sharma M. Reprogramming of antibiotics to combat antimicrobial resistance. Arch Pharm (Weinheim) 2020; 353:e2000168. [DOI: 10.1002/ardp.202000168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/04/2020] [Accepted: 07/11/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Kashyap K. Dubey
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
- School of Biotechnology Jawaharlal Nehru University New Delhi India
| | - Indu
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
| | - Manisha Sharma
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
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15
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Potential Antiviral Options against SARS-CoV-2 Infection. Viruses 2020; 12:v12060642. [PMID: 32545799 PMCID: PMC7354438 DOI: 10.3390/v12060642] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/18/2023] Open
Abstract
As of June 2020, the number of people infected with severe acute respiratory coronavirus 2 (SARS-CoV-2) continues to skyrocket, with more than 6.7 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. However, developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent sera and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here, we developed a neutralization assay using SARS-CoV-2 strain and Vero-E6 cells. We identified the most potent sera from recovered patients for the treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against the SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that a combination of orally available virus-directed nelfinavir and host-directed amodiaquine exhibited the highest synergy. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19.
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16
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Napoli E, Siracusa L, Ruberto G. New Tricks for Old Guys: Recent Developments in the Chemistry, Biochemistry, Applications and Exploitation of Selected Species from the Lamiaceae Family. Chem Biodivers 2020; 17:e1900677. [PMID: 31967708 DOI: 10.1002/cbdv.201900677] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Lamiaceae is one of the largest families of flowering plants comprising about 250 genera and over 7,000 species. Most of the plants of this family are aromatic and therefore important source of essential oils. Lamiaceae are widely used as culinary herbs and reported as medicinal plants in several folk traditions. In the Mediterranean area oregano, sage, rosemary, thyme and lavender stand out for geographical diffusion and variety of uses. The aim of this review is to provide recent data dealing with the phytochemical and pharmacological studies, and the more recent applications of the essential oils and the non-volatile phytocomplexes. This literature survey suggests how the deeper understanding of biomolecular processes in the health and food sectors as per as pest control bioremediation of cultural heritage, or interaction with human microbiome, fields, leads to the rediscovery and new potential applications of well-known plants.
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Affiliation(s)
- Edoardo Napoli
- Istituto del CNR di Chimica Biomolecolare, Via Paolo Gaifami, 18, IT-95126, Catania, Italy
| | - Laura Siracusa
- Istituto del CNR di Chimica Biomolecolare, Via Paolo Gaifami, 18, IT-95126, Catania, Italy
| | - Giuseppe Ruberto
- Istituto del CNR di Chimica Biomolecolare, Via Paolo Gaifami, 18, IT-95126, Catania, Italy
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17
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Discovery and development of safe-in-man broad-spectrum antiviral agents. Int J Infect Dis 2020; 93:268-276. [PMID: 32081774 PMCID: PMC7128205 DOI: 10.1016/j.ijid.2020.02.018] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
We reviewed the discovery and development process of broad-spectrum antiviral agents. We summarized the information on 120 safe-in-man agents in a freely accessible database. Further studies will increase the number of broad-spectrum antivirals, expand the spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections.
Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of the general population from emerging and re-emerging viral diseases, reinforcing the arsenal of available antiviral options. Here, we review discovery and development of BSAAs and summarize the information on 120 safe-in-man agents in a freely accessible database (https://drugvirus.info/). Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand the spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.
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18
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Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine. Viruses 2019; 11:v11100964. [PMID: 31635418 PMCID: PMC6832696 DOI: 10.3390/v11100964] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Viruses are the major causes of acute and chronic infectious diseases in the world. According to the World Health Organization, there is an urgent need for better control of viral diseases. Repurposing existing antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we identified novel activities of obatoclax and emetine against herpes simplex virus type 2 (HSV-2), echovirus 1 (EV1), human metapneumovirus (HMPV) and Rift Valley fever virus (RVFV) in cell cultures. Moreover, we demonstrated novel activities of emetine against influenza A virus (FLUAV), niclosamide against HSV-2, brequinar against human immunodeficiency virus 1 (HIV-1), and homoharringtonine against EV1. Our findings may expand the spectrum of indications of these safe-in-man agents and reinforce the arsenal of available antiviral therapeutics pending the results of further in vitro and in vivo tests.
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19
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Gazerani P. Identification of novel analgesics through a drug repurposing strategy. Pain Manag 2019; 9:399-415. [DOI: 10.2217/pmt-2018-0091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The identification of new indications for approved or failed drugs is a process called drug repositioning or drug repurposing. The motivation includes overcoming the productivity gap that exists in drug development, which is a high-cost–high-risk process. Repositioning also includes rescuing drugs that have safely entered the market but have failed to demonstrate sufficient efficiency for the initial clinical indication. Considering the high prevalence of chronic pain, the lack of sufficient efficacy and the safety issues of current analgesics, repositioning seems to be an attractive approach. This review presents example of drugs that already have been repositioned and highlights new technologies that are available for the identification of additional compounds to stimulate the curiosity of readers for further exploration.
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Affiliation(s)
- Parisa Gazerani
- Biomedicine, Department of Health Science & Technology, Aalborg University, Frederik Bajers Vej 3 B, 9220 Aalborg East, Denmark
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20
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Parvathaneni V, Kulkarni NS, Muth A, Gupta V. Drug repurposing: a promising tool to accelerate the drug discovery process. Drug Discov Today 2019; 24:2076-2085. [PMID: 31238113 DOI: 10.1016/j.drudis.2019.06.014] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/14/2019] [Accepted: 06/20/2019] [Indexed: 02/01/2023]
Abstract
Traditional drug discovery and development involves several stages for the discovery of a new drug and to obtain marketing approval. It is necessary to discover new strategies for reducing the drug discovery time frame. Today, drug repurposing has gained importance in identifying new therapeutic uses for already-available drugs. Typically, repurposing can be achieved serendipitously (unintentional fortunate observations) or through systematic approaches. Numerous strategies to discover new indications for FDA-approved drugs are discussed in this article. Drug repurposing has therefore become a productive approach for drug discovery because it provides a novel way to explore old drugs for new use but encounters several challenges. Some examples of different approaches are reviewed here.
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Affiliation(s)
- Vineela Parvathaneni
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
| | - Nishant S Kulkarni
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
| | - Aaron Muth
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
| | - Vivek Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA.
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