1
|
Huang CY, Metz A, Lange R, Artico N, Potot C, Hazemann J, Müller M, Dos Santos M, Chambovey A, Ritz D, Eris D, Meyer S, Bourquin G, Sharpe M, Mac Sweeney A. Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. Acta Crystallogr D Struct Biol 2024; 80:123-136. [PMID: 38289714 PMCID: PMC10836397 DOI: 10.1107/s2059798324000329] [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: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.
Collapse
Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Alexander Metz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Roland Lange
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Nadia Artico
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Céline Potot
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - Manon Müller
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | | | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Deniz Eris
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Solange Meyer
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - May Sharpe
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | |
Collapse
|
2
|
Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
Collapse
Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
3
|
Soleymani N, Ahmadi S, Shiri F, Almasirad A. QSAR and molecular docking studies of isatin and indole derivatives as SARS 3CL pro inhibitors. BMC Chem 2023; 17:32. [PMID: 37024955 PMCID: PMC10079496 DOI: 10.1186/s13065-023-00947-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
The 3C-like protease (3CLpro), known as the main protease of SARS-COV, plays a vital role in the viral replication cycle and is a critical target for the development of SARS inhibitor. Comparative sequence analysis has shown that the 3CLpro of two coronaviruses, SARS-CoV-2 and SARS-CoV, show high structural similarity, and several common features are shared among the substrates of 3CLpro in different coronaviruses. The goal of this study is the development of validated QSAR models by CORAL software and Monte Carlo optimization to predict the inhibitory activity of 81 isatin and indole-based compounds against SARS CoV 3CLpro. The models were built using a newer objective function optimization of this software, known as the index of ideality correlation (IIC), which provides favorable results. The entire set of molecules was randomly divided into four sets including: active training, passive training, calibration and validation sets. The optimal descriptors were selected from the hybrid model by combining SMILES and hydrogen suppressed graph (HSG) based on the objective function. According to the model interpretation results, eight synthesized compounds were extracted and introduced from the ChEMBL database as good SARS CoV 3CLpro inhibitor. Also, the activity of the introduced molecules further was supported by docking studies using 3CLpro of both SARS-COV-1 and SARS-COV-2. Based on the results of ADMET and OPE study, compounds CHEMBL4458417 and CHEMBL4565907 both containing an indole scaffold with the positive values of drug-likeness and the highest drug-score can be introduced as selected leads.
Collapse
Affiliation(s)
- Niousha Soleymani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Shahin Ahmadi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | | | - Ali Almasirad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| |
Collapse
|
4
|
Wan L, Wang X, Wang T, Yuan X, Liu W, Huang Y, Deng C, Cao S. Comparison of Target Pocket Similarity and Progress into Research on Inhibitors of Picornavirus 3C Proteases. Chem Biodivers 2023; 20:e202201100. [PMID: 36808685 DOI: 10.1002/cbdv.202201100] [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: 11/19/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/21/2023]
Abstract
The 3C protease (3C Pro) plays a significant role in the life cycle of picornaviruses from replication to translation, making it an attractive target for structure-based design of drugs against picornaviruses. The structurally related 3C-like protease (3CL Pro) is an important protein involved in the replication of coronaviruses. With the emergence of COVID-19 and consequent intensive research into 3CL Pro, development of 3CL Pro inhibitors has emerged as a popular topic. This article compares the similarities of the target pockets of various 3C and 3CL Pros from numerous pathogenic viruses. This article also reports several types of 3C Pro inhibitors that are currently undergoing extensive studies and introduces various structural modifications of 3C Pro inhibitors to provide a reference for the development of new and more effective inhibitors of 3C Pro and 3CL Pro.
Collapse
Affiliation(s)
- Li Wan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Tangle Wang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaolan Yuan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Wei Liu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Yan Huang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Changyong Deng
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Shuang Cao
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| |
Collapse
|
5
|
Soylu-Eter Ö, Duran GN, Özbil M, Göktaş F, Cihan-Üstündağ G, Karalı N. Antiviral activity and molecular modeling studies on 1H-indole-2,3-diones carrying a naphthalene moiety. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
|
6
|
Al-Harrasi A, Behl T, Upadhyay T, Chigurupati S, Bhatt S, Sehgal A, Bhatia S, Singh S, Sharma N, Vijayabalan S, Palanimuthu VR, Das S, Kaur R, Aleya L, Bungau S. Targeting natural products against SARS-CoV-2. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:42404-42432. [PMID: 35362883 PMCID: PMC8972763 DOI: 10.1007/s11356-022-19770-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/13/2022] [Indexed: 06/01/2023]
Abstract
The human coronavirus disease (COVID-19) pandemic is caused by a novel coronavirus; the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Natural products, secondary metabolites show positive leads with antiviral and immunotherapy treatments using genomic studies in silico docking. In addition, it includes the action of a mechanism targeting the SARS-CoV-2. In this literature, we aimed to evaluate the antiviral movement of the NT-VRL-1 unique terpene definition to Human coronavirus (HCoV-229E). The effects of 19 hydrolysable tannins on the SARS-CoV-2 were therefore theoretically reviewed and analyzed utilising the molecular operating surroundings for their C-Like protease 3CLpro catalytic dyad residues Angiotensin converting enzyme-2 (MOE 09). Pedunculagin, tercatan, and castalin were detected as interacting strongly with SARS-receptor Cov-2's binding site and catalytic dyad (Cys145 and His41). SARS-CoV-2 methods of subunit S1 (ACE2) inhibit the interaction of the receiver with the s-protein once a drug molecule is coupled to the s-protein and prevent it from infecting the target cells in alkaloids. Our review strongly demonstrates the evidence that natural compounds and their derivatives can be used against the human coronavirus and serves as an area of research for future perspective.
Collapse
Affiliation(s)
- Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mawz, Oman
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Tanuj Upadhyay
- Amity Institute of Pharmacy, Amity University, Gwalior, Madhya Pradesh, India
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah, Kingdom of Saudi Arabia
| | - Shvetank Bhatt
- Amity Institute of Pharmacy, Amity University, Gwalior, Madhya Pradesh, India
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mawz, Oman
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Shantini Vijayabalan
- Faculty of Health and Medical Sciences, School of Pharmacy, Taylor's University, Subang Jaya, Kuala Lumpur, Malaysia
| | - Vasanth Raj Palanimuthu
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Suprava Das
- Department of Pharmacology, Faculty of Medicine, AIMST University, Semeling, Bedong, Kedah, Malaysia
| | - Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| |
Collapse
|
7
|
Abu-Hashem AA, Al-Hussain SA. Design, Synthesis of New 1,2,4-Triazole/1,3,4-Thiadiazole with Spiroindoline, Imidazo[4,5-b]quinoxaline and Thieno[2,3-d]pyrimidine from Isatin Derivatives as Anticancer Agents. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030835. [PMID: 35164098 PMCID: PMC8839254 DOI: 10.3390/molecules27030835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
The current work aims to design and synthesis a new series of isatin derivatives and greatly enhances their cytotoxic activity. The derivatives 3-((bromophenyl) imino)-1-(morpholino (pyridine) methyl) indolin-2-one, 2-((oxoindoline) amino) benzoic acid, 3-(thiazolo-imino) indolinone, ethyl-2-((oxoindolin-3-ylidene)amino)-benzothiophene-3-carboxylate, 1-(oxoindoline)-benzo[4,5] thieno [2,3-d]pyrimidin-4(1H)-one, ethyl-2-(2-oxoindoline) hydrazine-1-carboxylate, N-(mercapto-oxo-pyrimidine)-2-(oxoindoline) hydrazine-1-carboxamide, N-(oxo-thiazolo[3,2-a] pyrimidine)-2-(oxoindolin-ylidene) hydrazine-carboxamide, 3-((amino-phenyl) amino)-3-hydroxy- indolinone, 3-((amino-phenyl) imino)-indolinone, 2-(2-((oxoindoline) amino) phenyl) isoindolinone, 2-(oxoindoline) hydrazine-carbothioamide, 5′-thioxospiro[indoline-3,3′-[1,2,4]triazolidin]-one, 5′-amino-spiro[indoline-3,2′-[1,3,4]thiadiazol]-2-one and 3-((2-thioxo-imidazo[4,5-b]quinoxaline) imino) indolinone were synthesized from the starting material 1-(morpholino (pyridine) methyl) indoline-2,3-dione and evaluated for their in vitro cytotoxic activity against carcinogenic cells. The new chemical structures were evidenced using spectroscopy (IR, NMR and MS) and elemental analysis. The results show that compounds imidazo[4,5-b]quinoxaline-indolinone, thiazolopyrimidine-oxoindoline, pyrimidine-oxoindoline-hydrazine-carboxamide, spiro[indoline-3,2′-[1,3,4] thiadiazol]-one and spiro[indoline-3,3′-[1,2,4]triazolidin]-one have excellent anti-proliferative activities against different human cancer cell lines such as gastric carcinoma cells (MGC-803), breast adenocarcinoma cells (MCF-7), nasopharyngeal carcinoma cells (CNE2) and oral carcinoma cells (KB).
Collapse
Affiliation(s)
- Ameen Ali Abu-Hashem
- Heterocyclic Unit, Photochemistry Department, National Research Centre, Dokki, Giza 12622, Egypt
- Chemistry Department, Faculty of Science, Jazan University, Jazan 45142, Saudi Arabia
- Correspondence: ; Tel.: +20-012-2521-1700; Fax: +20-2-3337-0931
| | - Sami A. Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13318, Saudi Arabia;
| |
Collapse
|
8
|
Elsaman T, Mohamed MS, Eltayib EM, Abdel-aziz HA, Abdalla AE, Munir MU, Mohamed MA. Isatin derivatives as broad-spectrum antiviral agents: the current landscape. Med Chem Res 2022; 31:244-273. [PMID: 35039740 PMCID: PMC8754539 DOI: 10.1007/s00044-021-02832-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023]
Abstract
In recent decades, several viruses have resulted in large outbreaks with serious health, economic and social consequences. The current unprecedented outbreak of the new coronavirus, SARS-COV-2, necessitates intensive efforts for delivering effective therapies to eradicate such a deadly virus. Isatin is an opulent heterocycle that has been proven to provide tremendous opportunities in the area of drug discovery. Over the last fifty years, suitably functionalized isatin has shown remarkable and broad-spectrum antiviral properties. The review herein is an attempt to compile all of the reported information about the antiviral activity of isatin derivatives with an emphasis on their structure-activity relationships (SARs) along with mechanistic and molecular modeling studies. In this regard, we are confident that the review will afford the scientific community a valuable platform to generate more potent and cost-effective antiviral therapies based on isatin templates.
Collapse
Affiliation(s)
- Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Malik Suliman Mohamed
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Eyman Mohamed Eltayib
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Hatem A. Abdel-aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622 Egypt
| | - Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Muhammad Usman Munir
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| |
Collapse
|
9
|
Utilization and simulation of innovative new binuclear Co(ii), Ni(ii), Cu(ii), and Zn(ii) diimine Schiff base complexes in sterilization and coronavirus resistance (Covid-19). OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This article aimed at the synthesis and molecular docking assessment of new diimine Schiff base ligand, namely 2-((E)-(2-((Z)-2-(4-chlorophenyl)-2-hydroxyvinyl)hydrazono) methyl)-6-methoxyphenol (methoxy-diim), via the condensation of 1-(4-chloro-phenyl)-2-hydrazino-ethenol compound with 2-((E)-(2-((Z)-2-(4-chlorophenyl)-2-hydroxy vinyl) hydrazono)methyl)-6-methoxyphenol in acetic acid as well as the preparation of new binuclear complexes of Co(ii), Ni(ii), Cu(ii), and Zn(ii). The following synthesized complexes were prepared in a ratio of 2:1 (metal/ligand). The 1H-NMR, UV-Vis, and FTIR spectroscopic data; molar conductivity measurements; and microanalytical, XRD, TGA/DTG, and biological studies were carried out to determine the molecular structure of these complexes. According to the spectroscopic analysis, the two central metal ions were coordinated with the diamine ligand via the nitrogen of the hydrazine and oxygen of the hydroxyl groups for the first metal ions and via the nitrogen of the hydrazine and oxygen of the phenol group for the second metal ions. Molecular docking for the free ligand was carried out against the breast cancer 3hb5-oxidoreductase and the 4o1v-protein binding kidney cancer and COVID-19 protease, and good results were obtained.
Collapse
|
10
|
Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. An Updated Review on SARS-CoV-2 Main Proteinase (M Pro): Protein Structure and Small-Molecule Inhibitors. Curr Top Med Chem 2021; 21:442-460. [PMID: 33292134 DOI: 10.2174/1568026620666201207095117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
[Coronaviruses (CoVs) are enveloped positive-stranded RNA viruses with spike (S) protein projections that allow the virus to enter and infect host cells. The S protein is a key virulence factor determining viral pathogenesis, host tropism, and disease pathogenesis. There are currently diverse corona viruses that are known to cause disease in humans. The occurrence of Middle East respiratory syndrome coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), as fatal human CoV diseases, has induced significant interest in the medical field. The novel coronavirus disease (COVID-19) is an infectious disease caused by a novel strain of coronavirus (SAR-CoV-2). The SARS-CoV2 outbreak has been evolved in Wuhan, China, in December 2019, and identified as a pandemic in March 2020, resulting in 53.24 M cases and 1.20M deaths worldwide. SARS-CoV-2 main proteinase (MPro), a key protease of CoV-2, mediates viral replication and transcription. SARS-CoV-2 MPro has been emerged as an attractive target for SARS-CoV-2 drug design and development. Diverse scaffolds have been released targeting SARS-CoV-2 MPro. In this review, we culminate the latest published information about SARS-CoV-2 main proteinase (MPro) and reported inhibitors.
Collapse
Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Haizhen A Zhong
- Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182, United States
| |
Collapse
|
11
|
Boozari M, Hosseinzadeh H. Natural products for
COVID
‐19 prevention and treatment regarding to previous coronavirus infections and novel studies. Phytother Res 2020; 35:864-876. [DOI: 10.1002/ptr.6873] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Motahareh Boozari
- Department of Pharmacognosy, School of Pharmacy Mashhad University of Medical Sciences Mashhad Iran
| | - Hossein Hosseinzadeh
- Department of Pharmacodynamics and Toxicology, School of Pharmacy Mashhad University of Medical Sciences Mashhad Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute Mashhad University of Medical Sciences Mashhad Iran
| |
Collapse
|
12
|
Ghosh AK, Brindisi M, Shahabi D, Chapman ME, Mesecar AD. Drug Development and Medicinal Chemistry Efforts toward SARS-Coronavirus and Covid-19 Therapeutics. ChemMedChem 2020; 15:907-932. [PMID: 32324951 PMCID: PMC7264561 DOI: 10.1002/cmdc.202000223] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 infection is spreading at an alarming rate and has created an unprecedented health emergency around the globe. There is no effective vaccine or approved drug treatment against COVID-19 and other pathogenic coronaviruses. The development of antiviral agents is an urgent priority. Biochemical events critical to the coronavirus replication cycle provided a number of attractive targets for drug development. These include, spike protein for binding to host cell-surface receptors, proteolytic enzymes that are essential for processing polyproteins into mature viruses, and RNA-dependent RNA polymerase for RNA replication. There has been a lot of ground work for drug discovery and development against these targets. Also, high-throughput screening efforts have led to the identification of diverse lead structures, including natural product-derived molecules. This review highlights past and present drug discovery and medicinal-chemistry approaches against SARS-CoV, MERS-CoV and COVID-19 targets. The review hopes to stimulate further research and will be a useful guide to the development of effective therapies against COVID-19 and other pathogenic coronaviruses.
Collapse
Affiliation(s)
- Arun K. Ghosh
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Medicinal Chemistry and Molecular PharmacolgyPurdue UniversityWest LafayetteIN 47907USA
| | - Margherita Brindisi
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Excellence of PharmacyUniversity of Naples Federico II80131NaplesItaly
| | - Dana Shahabi
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
| | | | - Andrew D. Mesecar
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of BiochemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Biological SciencesPurdue UniversityWest LafayetteIN 47907USA
| |
Collapse
|
13
|
More M, Joshi P, Mishra Y, Khanna P. Metal complexes driven from Schiff bases and semicarbazones for biomedical and allied applications: a review. MATERIALS TODAY. CHEMISTRY 2019; 14:100195. [PMID: 32289101 PMCID: PMC7110249 DOI: 10.1016/j.mtchem.2019.100195] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Accepted: 09/01/2019] [Indexed: 05/22/2023]
Abstract
Schiff bases are versatile organic compounds which are widely used and synthesized by condensation reaction of different amino compound with aldehydes or ketones known as imine. Schiff base ligands are considered as privileged ligands as they are simply synthesized by condensation. They show broad range of application in medicine, pharmacy, coordination chemistry, biological activities, industries, food packages, dyes, and polymer and also used as an O2 detector. Semicarbazone is an imine derivative which is derived from condensation of semicarbazide and suitable aldehyde and ketone. Imine ligand-containing transition metal complexes such as copper, zinc, and cadmium have shown to be excellent precursors for synthesis of metal or metal chalcogenide nanoparticles. In recent years, the researchers have attracted enormous attention toward Schiff bases, semicarbazones, thiosemicarbazones, and their metal complexes owing to numerous applications in pharmacology such as antiviral, antifungal, antimicrobial, antimalarial, antituberculosis, anticancer, anti-HIV, catalytic application in oxidation of organic compounds, and nanotechnology. In this review, we summarize the synthesis, structural, biological, and catalytic application of Schiff bases as well as their metal complexes.
Collapse
Key Words
- 2,6-DAPBPTSC, 2,6-diacetylpyridine bis-4-phenyl-3-thiosemicarbazone
- 35-DTBP, 3,5-di-tert-butylphenol
- 3CLpro, 3C-like protease
- ATNR, Amine terminated liquid natural rubber
- ATT, 2-acetylthiophene thiosemicarbazone
- BBPT, Biacetyl bis(4-phenyl-3-thiosemicarbazone)
- BBTSC, Benzyloxybenzaldehyde thiosemicarbazone
- BCG, Bacillus calmette-guérine
- BDT, Benzyldithiosemicarbazone
- BGPT, Bipyridyl glyoxal bis(4-phenyl-3-thiosemicarbazone)
- BMTS, Biacetyl monothiosemicarbazone
- Biological/biomedical activities
- Bipy, 2,2-bipyridine
- CT DNA, Calf thymus deoxyribonucleic acid
- DAPY, 2,3-diamino-pyridine
- DTBP, 2,6-di-tert-butylphenol
- DTBQ, 2,6-di-tert-butyl-4,4′-benzoquinone
- EAC, Enrichlish Ascitices Cells
- HEK-293, Human Embryonic Kidney cells
- HL-60, Human leukemia-60 cell line
- HeLa, immortal cell lines
- HepG2, Hepatic cellular carcinoma cells (Human liver cancer cell line)
- IgG, Immunoglobin G
- K B HCT-8, Human colon cancer cell line
- M-IBDET, N-methylisatin-β-4′,4′-diethylthiosemicarbazone
- MCF-7, Michigan Cancer Foundation-7
- MCF7 cells, Michigan Cancer Foundation-7 (breast cancer cell line)
- MHV, Mouse hepatitis virus
- MLV, Moloney leukemia virus
- MSOPD, N,N-bis(3-methylsalicylidene)-ortho-phenylenediamine
- Metal complexes
- NQSC, Naphthoquinone semicarbazone
- NQTS, ortho-Naphthoquinone thiosemicarbazone
- OLED, Organic light emitting diode
- PAS, p-amino salicylic acid
- PPTS, Picolinealdehyde-4-phenyl-3-thiosemicarbazone
- Phen, 1,10-phenanthroline
- SARS CoV, Severe Acute Respiratory Syndrome coronavirus
- SARS, Severe acute respiratory syndrome
- SB-HAG, Schiff bases of hydroxyamino guanidines
- SK-MEL-30, Human Melanoma Cell Line
- SK-OV-3 cells, Ovarian cancer cell line
- SSB-HAG, salicylaldehyde Schiff bases of HAG
- Schiff base
- Semicarbazone
- TCIDw, Tissue culture Infective Dose
- TTBDQ, 3,5,3′,5′-tetra-tert-butyl-4,4′-diphenoquinone
- VSV, vesicular stomatitis virus
- scCO2, Super-critical carbon dioxide
Collapse
Affiliation(s)
- M.S. More
- Nanochemistry/QDs R & D Laboratory, Department of Applied Chemistry, Defence Institute of Advanced Technology (DIAT), Ministry of Defence, DRDO, Government of India, Girinagar, Pune, 411025, India
| | - P.G. Joshi
- Nanochemistry/QDs R & D Laboratory, Department of Applied Chemistry, Defence Institute of Advanced Technology (DIAT), Ministry of Defence, DRDO, Government of India, Girinagar, Pune, 411025, India
| | - Y.K. Mishra
- Institute for Materials Science, Kiel University, Kaiserstrasse. 2, Kiel, 24143, Germany
- NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400, Sønderborg, Denmark
| | - P.K. Khanna
- Nanochemistry/QDs R & D Laboratory, Department of Applied Chemistry, Defence Institute of Advanced Technology (DIAT), Ministry of Defence, DRDO, Government of India, Girinagar, Pune, 411025, India
| |
Collapse
|
14
|
Varun, Sonam, Kakkar R. Isatin and its derivatives: a survey of recent syntheses, reactions, and applications. MEDCHEMCOMM 2019; 10:351-368. [PMID: 30996856 PMCID: PMC6438150 DOI: 10.1039/c8md00585k] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023]
Abstract
Isatin (1H-indole-2,3-dione) and its derivatives represent an important class of heterocyclic compounds that can be used as precursors for drug synthesis. Since its discovery, a lot of research work has been done regarding the synthesis, chemical properties, and biological and industrial applications of isatin. In this review, we have reported several novel methods for the synthesis of N-, C2-, and C3-substituted and spiro derivatives of isatin. The isatin moiety also shows important chemical reactions such as oxidation, ring expansion, Friedel-Crafts reaction and aldol condensation. These reactions, in turn, produce several biologically viable compounds like 2-oxindoles, tryptanthrin, indirubins, and many more. We have also summarized some recently reported biological activities exhibited by isatin derivatives, like anti-cancer, anti-bacterial, anti-diabetic and others. Special attention has been paid to their anti-cancer activity, and various anti-cancer targets such as histone deacetylase, carbonic anhydrase, tyrosine kinase, and tubulin have been discussed in detail. Other applications of isatin derivatives, such as in the dye industry and in corrosion prevention, have also been discussed.
Collapse
Affiliation(s)
- Varun
- Department of Chemistry , University of Delhi , India .
| | - Sonam
- Department of Chemistry , University of Delhi , India .
| | - Rita Kakkar
- Department of Chemistry , University of Delhi , India .
| |
Collapse
|
15
|
Banerjee K, Bhat R, Rao VUB, Nain A, Rallapalli KL, Gangopadhyay S, Singh RP, Banerjee M, Jayaram B. Toward development of generic inhibitors against the 3C proteases of picornaviruses. FEBS J 2019; 286:765-787. [PMID: 30461192 PMCID: PMC7164057 DOI: 10.1111/febs.14707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 09/20/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022]
Abstract
Development of novel antivirals, which requires knowledge of the viral life cycle in molecular detail, is a daunting task, involving extensive investments, and frequently resulting in failure. As there exist significant commonalities among virus families in the manner of host interaction, identifying and targeting common rather than specific features may lead to the development of broadly useful antivirals. Here, we have targeted the 3C protease of Hepatitis A Virus (HAV), a feco-orally transmitted virus of the family Picornaviridae, for identification of potential antivirals. The 3C protease is a viable drug target as it is required by HAV, as well as by other picornaviruses, for post-translational proteolysis of viral polyproteins and for inhibiting host innate immune pathways. Computational screening, followed by chemical synthesis and experimental validation resulted in identification of a few compounds which, at low micromolar concentrations, could inhibit HAV 3C activity. These compounds were further tested experimentally against the 3C protease of Human Rhinovirus, another member of the Picornaviridae family, with comparable results. Computational studies on 3C proteases from other members of the picornavirus family have indicated that the compounds identified could potentially be generic inhibitors for picornavirus 3C proteases.
Collapse
Affiliation(s)
- Kamalika Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Ruchika Bhat
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
| | | | - Anshu Nain
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Kartik Lakshmi Rallapalli
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Department of Chemistry and BiochemistryUniversity of California San Diego9500 Gilman DrLa JollaCA92093USA
| | - Sohona Gangopadhyay
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Chemical DivisionGeological Survey of India15‐16 Jhalana DungriWestern RegionJaipur302004India
| | - R. P. Singh
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
| | - Manidipa Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
| |
Collapse
|
16
|
Discovery of Novel Druggable Sites on Zika Virus NS3 Helicase Using X-ray Crystallography-Based Fragment Screening. Int J Mol Sci 2018; 19:ijms19113664. [PMID: 30463319 PMCID: PMC6274715 DOI: 10.3390/ijms19113664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/28/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
The flavivirus family contains several important human pathogens, such as Zika virus (ZIKV), dengue, West Nile, and Yellow Fever viruses, that collectively lead to a large, global disease burden. Currently, there are no approved medicines that can target these viruses. The sudden outbreak of ZIKV infections in 2015⁻2016 posed a serious threat to global public health. While the epidemic has receded, persistent reservoirs of ZIKV infection can cause reemergence. Here, we have used X-ray crystallography-based screening to discover two novel sites on ZIKV NS3 helicase that can bind drug-like fragments. Both sites are structurally conserved in other flaviviruses, and mechanistically significant. The binding poses of four fragments, two for each of the binding sites, were characterized at atomic precision. Site A is a surface pocket on the NS3 helicase that is vital to its interaction with NS5 polymerase and formation of the flaviviral replication complex. Site B corresponds to a flexible, yet highly conserved, allosteric site at the intersection of the three NS3 helicase domains. Saturation transfer difference nuclear magnetic resonance (NMR) experiments were additionally used to evaluate the binding strength of the fragments, revealing dissociation constants (KD) in the lower mM range. We conclude that the NS3 helicase of flaviviruses is a viable drug target. The data obtained open opportunities towards structure-based design of first-in-class anti-ZIKV compounds, as well as pan-flaviviral therapeutics.
Collapse
|
17
|
Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K. Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem Biol 2018; 13:2783-2793. [PMID: 30063823 DOI: 10.1021/acschembio.8b00701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progression of the disease remains uncertain. In addition, little is known about the spatiotemporal regulation of DJ-1, or the biochemical basis explaining its numerous biological functions. Progress has been hampered by the lack of inhibitors with precisely known mechanisms of action. Herein, we have employed biophysical methodologies and X-ray crystallography to identify and to optimize a family of compounds inactivating the critical Cys106 residue of human DJ-1. We demonstrate these compounds are potent inhibitors of various activities of DJ-1 in vitro and in cell-based assays. This study reports a new family of DJ-1 inhibitors with a defined mechanism of action, and contributes toward the understanding of the biological function of DJ-1.
Collapse
Affiliation(s)
- Shinya Tashiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jose M. M. Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Aki Tanabe
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | | | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
| |
Collapse
|
18
|
Chen G, Lin J, Zhang J, Wu Y, Gu X, Hao X, Zhang Y. Autocatalytic synthesis of 3-ethyl-3-hydroxy-indole-2-ones and their neuroprotection and antitumor activities' evaluation. CR CHIM 2018. [DOI: 10.1016/j.crci.2018.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
19
|
Schulz R, Atef A, Becker D, Gottschalk F, Tauber C, Wagner S, Arkona C, Abdel-Hafez AA, Farag HH, Rademann J, Wolber G. Phenylthiomethyl Ketone-Based Fragments Show Selective and Irreversible Inhibition of Enteroviral 3C Proteases. J Med Chem 2018; 61:1218-1230. [PMID: 29328649 DOI: 10.1021/acs.jmedchem.7b01440] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lead structure discovery mainly focuses on the identification of noncovalently binding ligands. Covalent linkage, however, is an essential binding mechanism for a multitude of successfully marketed drugs, although discovered by serendipity in most cases. We present a concept for the design of fragments covalently binding to proteases. Covalent linkage enables fragment binding unrelated to affinity to shallow protein binding sites and at the same time allows differentiated targeted hit verification and binding location verification through mass spectrometry. We describe a systematic and rational computational approach for the identification of covalently binding fragments from compound collections inhibiting enteroviral 3C protease, a target with high therapeutic potential. By implementing reactive groups potentially forming covalent bonds as a chemical feature in our 3D pharmacophore methodology, covalent binders were discovered by high-throughput virtual screening. We present careful experimental validation of the virtual hits using enzymatic assays and mass spectrometry unraveling a novel, previously unknown irreversible inhibition of the 3C protease by phenylthiomethyl ketone-based fragments. Subsequent synthetic optimization through fragment growing and reactivity analysis against catalytic and noncatalytic cysteines revealed specific irreversible 3C protease inhibition.
Collapse
Affiliation(s)
- Robert Schulz
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Amira Atef
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Daniel Becker
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Franziska Gottschalk
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Carolin Tauber
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Stefan Wagner
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Atef A Abdel-Hafez
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Hassan H Farag
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Jörg Rademann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| |
Collapse
|
20
|
Mohammadi MK. Solvent-free synthesis of oxovanadium (V) complexes with isatin base schiff ligands. INORG NANO-MET CHEM 2017. [DOI: 10.1080/24701556.2017.1284096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
21
|
Zhang Q, Cao R, Liu A, Lei S, Li Y, Yang J, Li S, Xiao J. Design, synthesis and evaluation of 2,2-dimethyl-1,3-dioxolane derivatives as human rhinovirus 3C protease inhibitors. Bioorg Med Chem Lett 2017; 27:4061-4065. [PMID: 28778471 DOI: 10.1016/j.bmcl.2017.07.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
The human rhinovirus (HRV) is the most significant cause of the common cold all over the world. The maturation and replication of this virus entirely depend on the activity of a virus-encoded 3C protease. Due to the high conservation among different serotypes and the minimal homology existing between 3C protease and known mammalian enzymes, 3C protease has been regarded as an attractive target for the treatment of HRV infections. In this study, we identified a novel (4R,5R)-N4-(2-((3-methoxyphenyl)amino)ethyl)-2,2-dimethyl-N5-(naphthalen-2-yl)-1,3-dioxolane-4,5-dicarboxamide (7a) to be a HRV 3C protease inhibitor via virtual screening. Further research has been focused on the design, synthesis and in vitro biological evaluation of 7a derivatives. The studies revealed that compound 7d has an IC50 value of 2.50±0.7µM against HRV 3C protease, and it thus could serve as a promising compound for the development of novel anti-rhinoviral medicines.
Collapse
Affiliation(s)
- Qiyan Zhang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China; Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Ruiyuan Cao
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - An Liu
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Shihai Lei
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Yuexiang Li
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Jingjing Yang
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Song Li
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China; Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Junhai Xiao
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| |
Collapse
|
22
|
Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding. Comput Biol Chem 2017; 71:117-128. [PMID: 29153890 DOI: 10.1016/j.compbiolchem.2017.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 12/21/2022]
Abstract
The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations for sulfonamide scaffold. We present here molecular dynamics-based pharmacophore modeling of caspase-3-isatin sulfonamide crystal structure, to elucidate the essential non-covalent contacts and its associated pharmacophore features necessary to ensure caspase-3 optimal binding. We performed 20ns long dynamics of this crystal structure to extract global conformation states and converted into structure-based pharmacophore hypotheses which were rigorously validated using an exclusive focussed library of experimental actives and inactives of sulfonamide class by Receiver Operating Characteristic (ROC) statistic. Eighteen structure-based pharmacophore hypotheses with better sensitivity and specificity measures (>0.6) were chosen which collectively showed the role of pocket residues viz. Cys163 (S1 sub-site; required for covalent and H bonding with Michael acceptor of inhibitors), His121 (S1; π stack with bicyclic isatin moiety), Gly122 (S1; H bond with carbonyl oxygen) and Tyr204 (S2; π stack with phenyl group of the isatin sulfonamide molecule) as stringent binding entities for enabling caspase-3 optimal binding. The introduction of spatial pharmacophore site points obtained from dynamics-based pharmacophore models in a virtual screening strategy will be helpful to screen and optimize molecules belonging to sulfonamide class of caspase-3 inhibitors.
Collapse
|
23
|
Zinc oxide surface: a versatile nanoplatform for solvent-free synthesis of diverse isatin derivatives. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.06.094] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
24
|
Pillaiyar T, Manickam M, Namasivayam V, Hayashi Y, Jung SH. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J Med Chem 2016; 59:6595-628. [PMID: 26878082 PMCID: PMC7075650 DOI: 10.1021/acs.jmedchem.5b01461] [Citation(s) in RCA: 509] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CL(pro), has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CL(pro) chemotherapies discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small molecule inhibitors of SARS-CoV 3CL(pro). Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
Collapse
Affiliation(s)
- Thanigaimalai Pillaiyar
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Manoj Manickam
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Vigneshwaran Namasivayam
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Yoshio Hayashi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Sang-Hun Jung
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| |
Collapse
|
25
|
Da Costa L, Roche M, Scheers E, Coluccia A, Neyts J, Terme T, Leyssen P, Silvestri R, Vanelle P. VP1 crystal structure-guided exploration and optimization of 4,5-dimethoxybenzene-based inhibitors of rhinovirus 14 infection. Eur J Med Chem 2016; 115:453-62. [PMID: 27049678 DOI: 10.1016/j.ejmech.2016.03.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 01/26/2023]
Abstract
Human rhinoviruses (HRV) are the predominant cause of common colds and flu-like illnesses, but are also responsible for virus-induced exacerbations of asthma and chronic obstructive pulmonary disease. However, to date, no drug has been approved yet for clinical use. In this study, we present the results of the structure-based lead optimization of a class of new small-molecule inhibitors that we previously reported to bind into the pocket beneath the canyon of the VP1 protein. A small series of analogues that we designed based on the available structure and interaction data were synthesized and evaluated for their potency to inhibit the replication of HRV serotype 14. 2-(4,5-Dimethoxy-2-nitrophenyl)-1-(4-(pyridin-4-yl)phenyl)ethanol (3v) was found to be a potent inhibitor exhibiting micromolar activity (EC50 = 3.4 ± 1.0 μM) with a toxicity for HeLa cells that was significantly lower than that of our previous hit (LPCRW_0005, CC50 = 104.0 ± 22.2 μM; 3v, CC50 > 263 μM).
Collapse
Affiliation(s)
- Laurène Da Costa
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Manon Roche
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Els Scheers
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Antonio Coluccia
- Institut Pasteur Italy, Department of Drug Chemistry and Technologies, Sapienza University, I-00185 Rome, Italy
| | - Johan Neyts
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium.
| | - Thierry Terme
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Pieter Leyssen
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Romano Silvestri
- Institut Pasteur Italy, Department of Drug Chemistry and Technologies, Sapienza University, I-00185 Rome, Italy.
| | - Patrice Vanelle
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France.
| |
Collapse
|
26
|
Kim BK, Cho JH, Jeong P, Lee Y, Lim JJ, Park KR, Eom SH, Kim YC. Benserazide, the first allosteric inhibitor of Coxsackievirus B3 3C protease. FEBS Lett 2015; 589:1795-801. [PMID: 26022398 PMCID: PMC7094222 DOI: 10.1016/j.febslet.2015.05.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/30/2015] [Accepted: 05/07/2015] [Indexed: 01/20/2023]
Abstract
Coxsackievirus B3 is the main cause of human viral myocarditis and cardiomyopathy. Virally encoded Coxsackievirus 3C protease (3C(pro)) plays an essential role in viral proliferation. Here, benserazide was discovered as a novel inhibitor from a drug library screen targeting Coxsackievirus 3C(pro) using a FRET-based enzyme assay. Benserazide, whose chemical structure has no electrophilic functional groups, was characterized as a non-competitive inhibitor by enzyme kinetic studies. A molecular docking study with benserazide and its analogs indicated that a novel putative allosteric binding site was involved. Specifically, a 2,3,4-trihydroxybenzyl moiety was determined to be a key pharmacophore for the enzyme's inhibitory activity. We suggest that the putative allosteric binding site may be a novel target for future therapeutic strategies.
Collapse
Affiliation(s)
- Bo-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju (GIST) 500-712, Republic of Korea
| | - Joong-Heui Cho
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 701-310, Republic of Korea
| | - Pyeonghwa Jeong
- Department of Medical System Engineering (DMSE), Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Youngjin Lee
- School of Life Sciences, Steitz Center for Structural Biology, Systems Biology Research Center and Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Jia Jia Lim
- School of Life Sciences, Steitz Center for Structural Biology, Systems Biology Research Center and Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Steitz Center for Structural Biology, Systems Biology Research Center and Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Soo Hyun Eom
- School of Life Sciences, Steitz Center for Structural Biology, Systems Biology Research Center and Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju (GIST) 500-712, Republic of Korea; Department of Medical System Engineering (DMSE), Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| |
Collapse
|
27
|
Dou X, Yao W, Jiang C, Lu Y. Enantioselective N-alkylation of isatins and synthesis of chiral N-alkylated indoles. Chem Commun (Camb) 2015; 50:11354-7. [PMID: 25163647 DOI: 10.1039/c4cc04586f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Asymmetric N-alkylations of isatins with enals were shown to be feasible via a prolinol-catalyzed iminium activation, and N-alkylated isatins were obtained in good yields and with excellent enantioselectivity. The biologically useful N-alkylated isatins also served as valuable synthetic precursors, and could be readily converted to chiral N-alkylated indole derivatives. The described method provides a novel entry to access optically enriched N-alkylated isatins and indole derivatives.
Collapse
Affiliation(s)
- Xiaowei Dou
- Department of Chemistry and Medicinal Chemistry Program, Life Sciences Institute, National University of Singapore, 3 Science Drive 3, Republic of Singapore 117543.
| | | | | | | |
Collapse
|
28
|
Deng JC, Chen WY, Zhu C, Chuang SC. Multicomponent Reactions of Phosphines, Enynedioates and Cinnamaldimines Give γ-Lactams with a 1,3,5-Hexatriene Moiety for Facile 6π Electrocyclization: Access to Oxindoles, Isatins and Isoxazolinones. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201401134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
29
|
Kuo C, Liang P. Characterization and Inhibition of the Main Protease of Severe Acute Respiratory Syndrome Coronavirus. CHEMBIOENG REVIEWS 2015. [PMCID: PMC7159133 DOI: 10.1002/cben.201400031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chih‐Jung Kuo
- National Chung Hsing University, College of Veterinary Medicine, Department of Veterinary Medicine, Taichung 402, Taiwan
| | - Po‐Huang Liang
- National Chung Hsing University, College of Veterinary Medicine, Department of Veterinary Medicine, Taichung 402, Taiwan
| |
Collapse
|
30
|
Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
31
|
Ilangovan A, Satish G. Direct Amidation of 2′-Aminoacetophenones Using I2-TBHP: A Unimolecular Domino Approach toward Isatin and Iodoisatin. J Org Chem 2014; 79:4984-91. [DOI: 10.1021/jo500550d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Andivelu Ilangovan
- School
of Chemistry, Bharathidasan University, Tiruchirappalli 620024, India
| | - Gandhesiri Satish
- School
of Chemistry, Bharathidasan University, Tiruchirappalli 620024, India
| |
Collapse
|
32
|
Synthesis, biological activity and structure–activity relationship of 4,5-dimethoxybenzene derivatives inhibitor of rhinovirus 14 infection. Eur J Med Chem 2014; 76:445-59. [DOI: 10.1016/j.ejmech.2014.01.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/14/2014] [Accepted: 01/18/2014] [Indexed: 11/23/2022]
|
33
|
Traube T, Shokhen M, Albeck A. A new method for filtering of reactive "warheads" of transition-state analog protease inhibitors. Eur J Med Chem 2014; 77:134-8. [PMID: 24631732 DOI: 10.1016/j.ejmech.2014.02.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
In light of the major contribution of the reactive warhead to the binding energy trend in reversible covalent transition-state analog inhibitors of serine and cysteine hydrolases, would it be possible to rationally design and quickly filter such warheads, especially for large-scale screening? The previously defined W1 and W2 covalent descriptors quantitatively account for the energetic effect of the covalent bonds reorganization, accompanying enzyme-inhibitor covalent binding. The quantum mechanically calculated W1 and W2 reflect the warhead binding energy by modeling of the enzyme-inhibitor reaction core. Here, we demonstrate the use of these descriptors for warhead filtering, and examine its scope and limitations. The W1 and W2 descriptors provide a tool for rational design of various warheads as universal building blocks of real inhibitors without the requirement of 3D structural information about the target enzyme or QSAR studies. These warheads could then be used as hit structural templates in the subsequent optimization of inhibitors recognition sites.
Collapse
Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
| |
Collapse
|
34
|
Synthesis, antitubercular and anticancer activity of new Baylis-Hillman adduct-derived N-cinnamyl-substituted isatin derivatives. Med Chem Res 2013; 23:1934-1940. [PMID: 32214765 PMCID: PMC7080103 DOI: 10.1007/s00044-013-0787-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/10/2013] [Indexed: 11/12/2022]
Abstract
Baylis–Hillman adduct-derived N-cinnamyl-substituted isatin derivatives were synthesized and evaluated for their antitubercular activity on Mycobacterium tuberculosis H37Rv strain ATCC 27294 by agar dilution method. Anticancer activity for the same compounds was also screened on four different cell lines: Chinese hamster ovary (CHO cells), Colo 205 (human colon cancer), Sup-T1 (human lymphoma) and C6 glioma (rat glioma) by MTT assay method. The compounds (3j–l) have shown significant activity against Mycobacterium strain and the compound 3l has shown specific cytotoxic activity.
Collapse
|
35
|
Pharmacophore modeling and docking studies on some nonpeptide-based caspase-3 inhibitors. BIOMED RESEARCH INTERNATIONAL 2013; 2013:306081. [PMID: 24089669 PMCID: PMC3780516 DOI: 10.1155/2013/306081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 11/17/2022]
Abstract
Neurodegenerative disorders are major consequences of excessive apoptosis caused by a proteolytic enzyme known as caspase-3. Therefore, caspase-3 inhibition has become a validated therapeutic approach for neurodegenerative disorders. We performed pharmacophore modeling on some synthetic derivatives of caspase-3 inhibitors (pyrrolo[3,4-c]quinoline-1,3-diones) using PHASE 3.0. This resulted in the common pharmacophore hypothesis AAHRR.6 which might be responsible for the biological activity: two aromatic rings (R) mainly in the quinoline nucleus, one hydrophobic (H) group (CH3), and two acceptor (A) groups (–C=O). After identifying a valid hypothesis, we also developed an atom-based 3D-QSAR model applying the PLS algorithm. The developed model was statistically robust (q2 = 0.53; pred_r2 = 0.80). Additionally, we have performed molecular docking studies, cross-validated our results, and gained a deeper insight into its molecular recognition process. Our developed model may serve as a query tool for future virtual screening and drug designing for this particular target.
Collapse
|
36
|
Synthesis, characterization, and antiviral activity of novel fluorinated isatin derivatives. MONATSHEFTE FUR CHEMIE 2013; 144:1725-1733. [PMID: 32214479 PMCID: PMC7087807 DOI: 10.1007/s00706-013-1034-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 06/09/2013] [Indexed: 10/27/2022]
Abstract
Abstract New series of Schiff's bases, hydrazones, thiosemicarbazones, thiazoles, and thiocarbohydrazones of 5-fluoroisatin were synthesized by the reaction of 5-fluoroisatin with primary amines, hydrazine hydrate, and thiocarbohydrazides. Thiosemicarbazones were prepared by reacting hydrazone derivatives with isothiocyanates. Upon treatment of thiosemicarbazone derivatives with chloroacetone, the thiazole derivatives were obtained. Some of the prepared compounds exhibited antiviral activity. Graphical abstract
Collapse
|
37
|
Ettari R, Tamborini L, Angelo IC, Micale N, Pinto A, De Micheli C, Conti P. Inhibition of Rhodesain as a Novel Therapeutic Modality for Human African Trypanosomiasis. J Med Chem 2013; 56:5637-58. [DOI: 10.1021/jm301424d] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Roberta Ettari
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Ilenia C. Angelo
- Dipartimento di Scienze del
Farmaco e Prodotti per la Salute, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Nicola Micale
- Dipartimento di Scienze del
Farmaco e Prodotti per la Salute, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Andrea Pinto
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Carlo De Micheli
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Paola Conti
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| |
Collapse
|
38
|
Schünemann K, Connelly S, Kowalczyk R, Sperry J, Wilson IA, Fraser JD, Brimble MA. A simple solid phase, peptide-based fluorescent assay for the efficient and universal screening of HRV 3C protease inhibitors. Bioorg Med Chem Lett 2012; 22:5018-24. [PMID: 22763202 DOI: 10.1016/j.bmcl.2012.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/06/2012] [Indexed: 11/30/2022]
Abstract
With over a 100 different serotypes, the human rhinovirus (HRV) is the major aetiological agent for the common cold, for which only symptomatic treatment is available. HRV maturation and replication is entirely dependent on the activity of a virally encoded 3C protease that represents an attractive target for the development of therapeutics to treat the common cold. Although a variety of small molecules and peptidomimetics have been found to inhibit HRV 3C protease, no universally compatible assay exists to reliably quantify the activity of the enzyme in vitro. Herein we report the development of a universal and robust solid phase peptide assay that utilizes the full HRV-14 3C protease recognition sequence and the release of 5(6)-carboxyfluorescein to sensitively quantify protease activity. This novel assay overcomes several limitations of existing assays allowing for the simple and efficient analysis of HRV-14 3C protease activity facilitating both high-throughput screening and the accurate kinetic study of HRV-14 3C protease inhibitors.
Collapse
Affiliation(s)
- Katrin Schünemann
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | | | | | | | | |
Collapse
|
39
|
Synthesis, biological activity and docking study of some new isatin Schiff base derivatives. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9896-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
40
|
El-Sayed WA, Abdel Megeid RE, Abbas HAS. Synthesis and antimicrobial activity of new 1-[(tetrazol-5-yl)methyl] indole derivatives, their 1,2,4-triazole thioglycosides and acyclic analogs. Arch Pharm Res 2011; 34:1085-96. [PMID: 21811915 DOI: 10.1007/s12272-011-0706-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 11/11/2010] [Accepted: 12/20/2010] [Indexed: 10/17/2022]
Abstract
New 1-[(tetrazol-5-yl)methyl]indole derivatives, their acyclic nucleoside analogs and the corresponding glycoside derivatives were synthesized. Furthermore, the [)(1,2,4-triazol-3-yl)methyl])-2H-tetrazole derivative as well as the corresponding thioglucoside were prepared. The synthesized compounds were tested for their antimicrobial activity against Aspergillus Niger, Penicillium sp, Candida albican, Bacillus subtilis, Streptococcus lacti, Escherichia coli, Pseudomonas sp., and streptomyces sp. Compounds 3, 5 and 19b exhibited potent antibacterial activity and compounds 4, 5 and 10 exhibited high activities against the tested fungi compared with fusidic acid.
Collapse
Affiliation(s)
- Weal A El-Sayed
- Photochemistry Department, National Research Center, El-Dokki, Cairo 72427, Egypt.
| | | | | |
Collapse
|
41
|
Chen G, Wang Y, Hao X, Mu S, Sun Q. Simple isatin derivatives as free radical scavengers: Synthesis, biological evaluation and structure-activity relationship. Chem Cent J 2011; 5:37. [PMID: 21722377 PMCID: PMC3150235 DOI: 10.1186/1752-153x-5-37] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 07/01/2011] [Indexed: 11/10/2022] Open
Abstract
To develop more potent small molecules with enhanced free radical scavenger properties, a series of N-substituted isatin derivatives was synthesized, and the cytoprotective effect on the apoptosis of PC12 cells induced by H2O2 was screened. All these compounds were found to be active, and N-ethyl isatin was found with the most potent activity of 69.7% protective effect on PC12 cells. Structure-activity relationship analyses showed the bioactivity of N-alkyl isatins decline as the increasing of the chain of the alkyl group, furthermore odd-even effect was found in the activity, which is interesting for further investigation.
Collapse
Affiliation(s)
- Gang Chen
- Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, PR China.
| | | | | | | | | |
Collapse
|
42
|
Singh VP, Singh S, Singh DP. Synthesis, characterization and biocidal activity of some transition metal(II) complexes with isatin salicylaldehyde acyldihydrazones. J Enzyme Inhib Med Chem 2011; 27:319-29. [DOI: 10.3109/14756366.2011.588228] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vinod P. Singh
- Department of Chemistry, Banaras Hindu University,
Varanasi, India
| | - Shweta Singh
- Department of Chemistry, Banaras Hindu University,
Varanasi, India
| | - Divya P. Singh
- Department of Chemistry, Banaras Hindu University,
Varanasi, India
| |
Collapse
|
43
|
Novel thiolactone–isatin hybrids as potential antimalarial and antitubercular agents. Bioorg Med Chem Lett 2011; 21:2055-8. [DOI: 10.1016/j.bmcl.2011.02.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 01/29/2011] [Accepted: 02/02/2011] [Indexed: 11/20/2022]
|
44
|
Baxter A, Chambers M, Edfeldt F, Edman K, Freeman A, Johansson C, King S, Morley A, Petersen J, Rawlins P, Spadola L, Thong B, Van de Poël H, Williams N. Non-covalent inhibitors of rhinovirus 3C protease. Bioorg Med Chem Lett 2011; 21:777-80. [PMID: 21183345 DOI: 10.1016/j.bmcl.2010.11.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 11/30/2022]
Abstract
The first known non-covalent inhibitors of rhinovirus 3C protease (3CP) have been identified through fragment based screening and hit identification activities.
Collapse
Affiliation(s)
- Andrew Baxter
- AstraZeneca, R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Malhotra S, Balwani S, Dhawan A, Singh BK, Kumar S, Thimmulappa R, Biswal S, Olsen CE, Van der Eycken E, Prasad AK, Ghosh B, Parmar VS. Synthesis and biological activity evaluation of N-protected isatin derivatives as inhibitors of ICAM-1 expression on human endothelial cells. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00262c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Banerjee D, Yogeeswari P, Bhat P, Thomas A, Srividya M, Sriram D. Novel isatinyl thiosemicarbazones derivatives as potential molecule to combat HIV-TB co-infection. Eur J Med Chem 2011; 46:106-21. [PMID: 21093117 DOI: 10.1016/j.ejmech.2010.10.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 01/30/2023]
|
47
|
Traube T, Vijayakumar S, Hirsch M, Uritsky N, Shokhen M, Albeck A. EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors. J Chem Inf Model 2010; 50:2256-65. [PMID: 21090595 DOI: 10.1021/ci100330y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We introduce an enzyme mechanism-based method (EMBM) aimed at rational design of chemical sites (CS) of reaction coordinate analog inhibitors. The energy of valence reorganization of CS, caused by the formation of the enzyme-inhibitor covalent complex, is accounted for by new covalent descriptors W1 and W2. We considered CS fragments with a carbonyl reactivity center, like in native protease substrates. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex, anionic TC(O-) or neutral TC(OH). The modeling on a reaction core allows generation of various CS and corresponding TC(O-) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine or cysteine hydrolases. Moreover, the approach avoids the need for 3D structure of the target enzyme, so EMBM may be used for ligand-based design. We have built a chemical site of inhibitors (CSI) databank with pairs of W1 and W2 descriptors precalculated for both CH₃O(-) and CH₃S(-) nucleophiles for every collected CS fragment. We demonstrated that contribution of a CS fragment to the binding affinity of an inhibitor depends on both its covalent reorganization during the chemical transformation and its noncovalent interactions in the enzyme active site. Consequently, prediction of inhibitors binding trend can be done only by accounting for all of these factors, using W1 and W2 in combination with noncovalent QSAR descriptors.
Collapse
Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | | | | | | | | | | |
Collapse
|
48
|
Kashanian S, Khodaei MM, Pakravan P. Spectroscopic Studies on the Interaction of Isatin with Calf Thymus DNA. DNA Cell Biol 2010; 29:639-46. [DOI: 10.1089/dna.2010.1054] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Soheila Kashanian
- Department of Chemistry, Faculty of Science, Sensor and Biosensor Research Center (SBRC) & Nanoscience and Nanotechnology Research Center (NNRC), Razi University, Kermanshah, Iran
| | - Mohammad Mehdi Khodaei
- Department of Chemistry, Faculty of Science, Sensor and Biosensor Research Center (SBRC) & Nanoscience and Nanotechnology Research Center (NNRC), Razi University, Kermanshah, Iran
| | - Parvaneh Pakravan
- Department of Chemistry, Faculty of Science, Razi University, Kermanshah, Iran
| |
Collapse
|
49
|
Kassab SE, Hegazy GH, Eid NM, Amin KM, El-Gendy AA. Synthesis of 1H-indole-2,3-dione-3-thiosemicarbazone ribonucleosides as antibacterial agents. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 29:72-80. [PMID: 20391194 DOI: 10.1080/15257770903459267] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A new isatin ribonucleoside (3) was synthesized in a good yield by trimethylsilyl trifluoromethanesulfonate (TMSOTf) catalyzed coupling reaction between the silylated nitrogenated base of 1H-Indole-2,3-dione (1) and 1,2,3,5-tetra-O-acetyl-beta-D-ribfuranose (2). Thiosemicarbazides 4a-e were utilized by the prepared ribonucleoside (3) to give new series of 1H-indole-2,3-dione-3-thiosemicarbazone ribonucleosides 5a-e. All compounds tested as antibacterial agents showed slight inhibitory activity against the selected bacterial strains.
Collapse
Affiliation(s)
- Shaymaa E Kassab
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Misr International University, Cairo, Egypt
| | | | | | | | | |
Collapse
|
50
|
Synthesis, characterization, and in vitro antimicrobial evaluation of hydrazone and bishydrazone derivatives of isatin. Pharm Chem J 2010. [DOI: 10.1007/s11094-010-0436-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|