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Feng R, Sun B, Zhang S, Su E, Kovalevsky A, Zhang F, Bennett BC, Shen Q, Wan Q. Discovery of Novel Rhizoctonia solani DHFR Inhibitors as Fungicides Using Virtual Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19385-19395. [PMID: 38038282 DOI: 10.1021/acs.jafc.3c05216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Dihydrofolate reductase (DHFR) is an essential enzyme in the folate pathway and has been recognized as a well-known target for antibacterial and antifungal drugs. We discovered eight compounds from the ZINC database using virtual screening to inhibit Rhizoctonia solani (R. solani), a fungal pathogen in crops. These compounds were evaluated with in vitro assays for enzymatic and antifungal activity. Among these, compound Hit8 is the most active R. solani DHFR inhibitor, with the IC50 of 10.2 μM. The selectivity of inhibition is 22.3 against human DHFR with the IC50 of 227.7 μM. Moreover, Hit8 has higher antifungal activity against R. solani (EC50 of 38.2 mg L-1) compared with validamycin A (EC50 of 67.6 mg L-1), a well-documented fungicide. These results suggest that Hit8 may be a potential fungicide. Our study exemplifies a computer-aided method to discover novel inhibitors that could target plant pathogenic fungi.
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Affiliation(s)
- Ruirui Feng
- College of Science, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Bo Sun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Shengkai Zhang
- Institute of Advanced Science Facilities, Shenzhen 518107, People's Republic of China
| | - Erzheng Su
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Feng Zhang
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Brad C Bennett
- Biological and Environmental Science Department, Samford University, Birmingham, Alabama 35229, United States
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qun Wan
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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Sehrawat R, Rathee P, Rathee P, Khatkar S, Akkol EK, Khatkar A, Sobarzo-Sánchez E. In silico design of novel bioactive molecules to treat breast cancer with chlorogenic acid derivatives: a computational and SAR approach. Front Pharmacol 2023; 14:1266833. [PMID: 38152692 PMCID: PMC10751932 DOI: 10.3389/fphar.2023.1266833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/19/2023] [Indexed: 12/29/2023] Open
Abstract
Introduction: Cancer is a vast group of diseases comprising abnormal cells that multiply and grow uncontrollably, and it is one of the top causes of death globally. Several types of cancers are diagnosed, but the incidence of breast cancer, especially in postmenopausal women, is increasing daily. Chemotherapeutic agents used to treat cancer are generally associated with severe side effects on host cells, which has led to a search for safe and potential alternatives. Therefore, the present research has been conducted to find novel bioactive molecules to treat breast cancer with chlorogenic acid and its derivatives. Chlorogenic acid was selected because of its known activity in the field. Methods: Several chlorogenic acid derivatives were subjected to computational studies such as molecular docking, determination of absorption, distribution, metabolism, and excretion (ADME), druglikeness, toxicity, and prediction of activity spectra for substances (PASS) to develop a potential inhibitor of breast cancer. The Protein Data Bank (PDB) IDs used for docking purposes were 7KCD, 3ERT, 6CHZ, 3HB5, and 1U72. Result: Exhaustive analysis of results has been conducted by considering various parameters, like docking score, binding energy, types of interaction with important amino acid residues in the binding pocket, ADME, and toxicity data of compounds. Among all the selected derivatives, CgE18, CgE11, CgAm13, CgE16, and CgE9 have astonishing interactions, excellent binding energy, and better stability in the active site of targeted proteins. The docking scores of compound CgE18 were -11.63 kcal/mol, -14.15 kcal/mol, and -12.90 kcal/mol against breast cancer PDB IDs 7KCD, 3HB5, and 1U72, respectively. The docking scores of compound CgE11 were -10.77 kcal/mol and -9.11 kcal/mol against breast cancer PDB IDs 3ERT and 6CHZ, respectively, whereas the docking scores of epirubicin hydrochloride were -3.85 kcal/mol, -6.4 kcal/mol, -8.76 kcal/mol, and -10.5 kcal/mol against PDB IDs 7KCD, 3ERT, 6CHZ, and 3HB5. The docking scores of 5-fluorouracil were found to be -5.25 kcal/mol, -3.43 kcal/mol, -3.73 kcal/mol, and -5.29 kcal/mol against PDB IDs 7KCD, 3ERT, 6CHZ, and 3HB5, which indicates the designed compounds have a better docking score than some standard drugs. Conclusion: Taking into account the results of molecular docking, drug likeness analysis, absorption, distribution, metabolism, excretion, and toxicity (ADMET) evaluation, and PASS, it can be concluded that chlorogenic acid derivatives hold promise as potent inhibitors for the treatment of breast cancer.
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Affiliation(s)
- Renu Sehrawat
- School of Medical and Allied Sciences, K. R. Mangalam University, Gurugram, Haryana, India
| | - Priyanka Rathee
- Faculty of Pharmaceutical Sciences, Baba Mastnath University, Rohtak, India
| | - Pooja Rathee
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Sarita Khatkar
- Vaish Institute of Pharmaceutical Education and Research, Rohtak, Haryana, India
| | - Esra Küpeli Akkol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara, Türkiye
| | - Anurag Khatkar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago, Chile
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
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Ramharack P, Salifu EY, Agoni C. Dual-Target Mycobacterium tuberculosis Inhibition: Insights into the Molecular Mechanism of Antifolate Drugs. Int J Mol Sci 2023; 24:14021. [PMID: 37762327 PMCID: PMC10530724 DOI: 10.3390/ijms241814021] [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: 07/10/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The escalating prevalence of drug-resistant strains of Mycobacterium tuberculosis has posed a significant challenge to global efforts in combating tuberculosis. To address this issue, innovative therapeutic strategies are required that target essential biochemical pathways while minimizing the potential for resistance development. The concept of dual targeting has gained prominence in drug discovery against resistance bacteria. Dual targeting recognizes the complexity of cellular processes and disrupts more than one vital pathway, simultaneously. By inhibiting more than one essential process required for bacterial growth and survival, the chances of developing resistance are substantially reduced. A previously reported study investigated the dual-targeting potential of a series of novel compounds against the folate pathway in Mycobacterium tuberculosis. Expanding on this study, we investigated the predictive pharmacokinetic profiling and the structural mechanism of inhibition of UCP1172, UCP1175, and UCP1063 on key enzymes, dihydrofolate reductase (DHFR) and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate reductase (RV2671), involved in the folate pathway. Our findings indicate that the compounds demonstrate lipophilic physiochemical properties that promote gastrointestinal absorption, and may also inhibit the drug-metabolizing enzyme, cytochrome P450 3A4, thus enhancing their biological half-life. Furthermore, key catalytic residues (Serine, Threonine, and Aspartate), conserved in both enzymes, were found to participate in vital molecular interactions with UCP1172, which demonstrated the most favorable free binding energies to both DHFR and RV2671 (-41.63 kcal/mol, -48.04 kcal/mol, respectively). The presence of characteristic loop shifts, which are similar in both enzymes, also indicates a common inhibitory mechanism by UCP1172. This elucidation advances the understanding of UCP1172's dual inhibition mechanism against Mycobacterium tuberculosis.
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Affiliation(s)
- Pritika Ramharack
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
- Discipline of Pharmaceutical Sciences, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Elliasu Y. Salifu
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
| | - Clement Agoni
- Discipline of Pharmaceutical Sciences, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Belfield, Ireland
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Reang J, Sharma K, Sharma PC, Yadav V, Sharma V, Majeed J. Discovery of VEGFR inhibitors through virtual screening and energy assessment. J Biochem Mol Toxicol 2023; 37:e23321. [PMID: 36808794 DOI: 10.1002/jbt.23321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/05/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) is crucial in promoting tumor angiogenesis and cancer metastasis. Thus, inhibition of VEGFR-2 has appeared as a good tactic for cancer treatment. To find out novel VEGFR-2 inhibitors, first, the PDB structure of VEGFR-2, 6GQO, was selected based on atomic nonlocal environment assessment (ANOLEA) and PROCHECK assessment. 6GQO was then further used for structure-based virtual screening (SBVS) of different molecular databases, including US-FDA approved drugs, US-FDA withdrawn drugs, may bridge, MDPI, and Specs databases using Glide. Based on SBVS, receptor fit, drug-like filters, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of 427877 compounds, the best 22 hits were selected. From the 22 hits, hit 5 complex with 6GQO was put through molecular mechanics/generalized born surface area (MM/GBSA) study and hERG binding. The MM/GBSA study revealed that hit 5 possesses lesser binding free energy with more inferior stability in the receptor pocket than the reference compound. The VEGFR-2 inhibition assay of hit 5 disclosed an IC50 of 165.23 nM against VEGFR-2, which can be possibly enhanced through structural modifications.
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Affiliation(s)
- Jurnal Reang
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Prabodh C Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Vivek Yadav
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Vinita Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Jaseela Majeed
- Department of Pharmaceutical Management, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
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Sabt A, Eldehna WM, Ibrahim TM, Bekhit AA, Batran RZ. New antileishmanial quinoline linked isatin derivatives targeting DHFR-TS and PTR1: Design, synthesis, and molecular modeling studies. Eur J Med Chem 2023; 246:114959. [PMID: 36493614 DOI: 10.1016/j.ejmech.2022.114959] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
In a search for new drug candidates for one of the neglected tropical diseases, leishmaniasis, twenty quinoline-isatin hybrids were synthesized and tested for their in vitro antileishmanial activity against Leishmaniamajor strain. All the synthesized compounds showed promising in vitro activity against the promastigote form in a low micromolar range (IC50 = 0.5084-5.9486 μM) superior to the reference miltefosine (IC50 = 7.8976 μM). All the target compounds were then tested against the intracellular amastigote form and showed promising inhibition effects (IC50 = 0.60442-8.2948 μM versus 8.08 μM for miltefosine). Compounds 4e, 4b and 4f were shown to possess the highest antileishmanial activity against both promastigote and amastigote forms. The most active compounds were proven to exhibit their significant antileishmanial effects through antifolate mechanism, targeting DHFR-TS and PTR1. To evaluate the safety profile of the most active derivatives 4e, 4b and 4f, the in vitro cytotoxicity test was carried out and displayed higher selectivity indices than the reference miltefosine. Molecular docking within putative target protein PTR1 confirmed the high potentiality of the most active compounds 4e, 4b and 4f to block the catalytic activity of Lm-PTR1.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt; School of Biotechnology, Badr University in Cairo, Badr City, 11829, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt; Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
| | - Adnan A Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Pharmacy Program, Allied Health Department, College of Health Sciences, University of Bahrain, P.O. Box 32038, Bahrain
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt.
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Bhagat K, Kumar N, Kaur Gulati H, Sharma A, Kaur A, Singh JV, Singh H, Bedi PMS. Dihydrofolate reductase inhibitors: patent landscape and phases of clinical development (2001-2021). Expert Opin Ther Pat 2022; 32:1079-1095. [PMID: 36189616 DOI: 10.1080/13543776.2022.2130752] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Dihydrofolate reductase (DHFR) plays an important role in the biosynthesis of amino acid and folic acid. It participates by reducing dihydrofolate to tetrahydrofolate, in the presence of nicotinamide dinucleotide phosphate cofactor, and has been verified by various clinical studies to use DHFR as a target for the treatment of cancer and various bacterial infections. AREA COVERED In this review, we have disclosed patents of synthetics and natural DHFR inhibitors with diaminopyrimidine and quinazoline nucleus from 2001. Additionally, this review highlights the clinical progression of numerous DHFR inhibitors received from the last five years. EXPERT OPINION From 2001 to 2021, numerous active chemical scaffolds have been introduced and are exposed as lead candidates that have entered clinical trials as potent DHFR inhibitors. Moreover, researchers have paid considerable attention to the development of a new class of DHFR inhibitors with higher selectivity and potency. This development includes synthesis of synthetic as well as natural compounds that are potent DHFR inhibitors. On the basis of literature review, we can anticipate that there are a huge number of novel active molecules available for the future that could possess superior abilities to target this enzyme with a profound pharmacological profile.
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Affiliation(s)
- Kavita Bhagat
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India.,Department of Pharmaceutical Sciences, Khalsa College of Pharmacy, Amritsar, India
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | | | - Aanchal Sharma
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Amandeep Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Jatinder Vir Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Harbinder Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
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Bajad NG, Singh SK, Singh SK, Singh TD, Singh M. Indole: A promising scaffold for the discovery and development of potential anti-tubercular agents. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100119. [PMID: 35992375 PMCID: PMC9389259 DOI: 10.1016/j.crphar.2022.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/13/2022] [Accepted: 07/05/2022] [Indexed: 11/08/2022] Open
Abstract
Indole-containing small molecules have been reported to have diverse pharmacological activities. The aromatic heterocyclic scaffold, which resembles various protein structures, has received attention from organic and medicinal chemists. Exploration of indole derivatives in drug discovery has rapidly yielded a vast array of biologically active compounds with broad therapeutic potential. Nature is the major source of indole scaffolds, but various classical and advanced synthesis methods for indoles have also been reported. One-pot synthesis is widely considered an efficient approach in synthetic organic chemistry and has been used to synthesize some indole compounds. The rapid emergence of drug-resistant tuberculosis is a major challenge to be addressed. Identifying novel targets and drug candidates for tuberculosis is therefore crucial. Researchers have extensively explored indole derivatives as potential anti-tubercular agents or drugs. Indole scaffolds containing the novel non-covalent (decaprenylphosphoryl-β-D-ribose2′-epimerase) DprE1 inhibitor 1,4-azaindole is currently in clinical trials to treat Mycobacterium tuberculosis. In addition, DG167 indazole sulfonamide with potent anti-tubercular activity is undergoing early-stage development in preclinical studies. Indole bearing cationic amphiphiles with high chemical diversity have been reported to depolarize and disrupt the mycobacterial membrane. Some indole-based compounds have potential inhibitory activities against distinct anti-tubercular targets, including the inhibition of cell wall synthesis, replication, transcription, and translation, as summarized in the graphical abstract. The success of computer-aided drug design in the fields of cancer and anti-viral drugs has accelerated in silico studies in antibacterial drug development. This review describes the sources of indole scaffolds, the potential for novel indole derivatives to serve as anti-tubercular agents, in silico findings, and proposed actions to facilitate the design of novel compounds with anti-tubercular activity. The Indole derivatives emerged as an efficient bioactive compoundes with wide range of therapeutic potential. Identifying novel drug candidates with indole derivatives can curtail the rapid emergence of drug-resistant tuberculosis. The current review highlights the sources of indole scaffolds, their derivatives, and in silico findings as anti-tubercular agents. Currently, DprE1 inhibitor 1,4-azaindole and DG167 indazole sulfonamide are in clinical trials to treat Mycobacterium tuberculosis.
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Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. Int J Mol Sci 2021; 22:ijms222413259. [PMID: 34948055 PMCID: PMC8703488 DOI: 10.3390/ijms222413259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
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Chawla P, Teli G, Gill RK, Narang RK. An Insight into Synthetic Strategies and Recent Developments of Dihydrofolate Reductase Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202102555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pooja Chawla
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
- Pooja Chawla Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga 142001 Punjab India
| | - Ghanshyam Teli
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
| | - Rupinder Kaur Gill
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
| | - Raj Kumar Narang
- Department of Pharmaceutics ISF College of Pharmacy Moga Punjab India
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Atukuri D, Gunjal R, Holagundi N, Korlahalli B, Gangannavar S, Akkasali K. Contribution of N-heterocycles towards anti-tubercular drug discovery (2014-2019); predicted and reengineered molecular frameworks. Drug Dev Res 2021; 82:767-783. [PMID: 33660325 DOI: 10.1002/ddr.21809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 11/08/2022]
Abstract
Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis, responsible for high death frequency every year all over the world. In this regard, efficient drug-design and discovery towards the prevention of M.tb H37 Rv is of prime concern. Prevention of the infection may include vaccination, and the treatment comprises anti-TB drug regimen. However, the vaccine decreases the risk of tuberculosis infection only to some extent, while drug-resistance limits the efficacy of the existing anti-TB agents. Much improvement has to be achieved to overcome pitfalls such as side effects, high-toxicity, low bioavailability, pharmacokinetics and pharmacodynamics, and hence forth in clinical therapeutics. Amongst heterocyclic compounds, N-heterocycles played a pivotal role in drug-design and discovery. A wide range of microbial diseases are being treated by the N-heterocyclic drugs. The present review comprises description of anti-TB effects of the N-heterocycles such as indoles, triazoles, thiazoles, and pyrazoles. The potent anti-TB activity exerted by the derivatives of these heterocycles is evaluated critically alongside emphasizing structure-activity relationship. Besides, docking studies supporting anti-TB activity is supplemented. Alongside this, based on the potent heterocyclic molecules, the molecular frameworks are designed that would bring about enhanced M. tb H37 Rv inhibitory potencies.
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Affiliation(s)
- Dorababu Atukuri
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Rutu Gunjal
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Nagaraj Holagundi
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | | | | | - Kirankumar Akkasali
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
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Exploration of carbamide derived pyrimidine-thioindole conjugates as potential VEGFR-2 inhibitors with anti-angiogenesis effect. Eur J Med Chem 2020; 200:112457. [PMID: 32422489 DOI: 10.1016/j.ejmech.2020.112457] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/28/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022]
Abstract
The development of new small molecules from known structural motifs through molecular hybridization is one of the trends in drug discovery. In this connection, we have combined the two pharmacophoric units (pyrimidine and thioindole) in a single entity via molecular hybridization strategy along with introduction of urea functionality at C2 position of pyrimidine to increase the efficiency of H-bonding interactions. Among the synthesized conjugates 12a-aa, compound 12k was found to exhibit significant IC50 values 5.85, 7.87, 6.41 and 10.43 μM against MDA-MB-231 (breast), HepG2 (liver), A549 (lung) and PC-3 (prostate) cancer cell lines, respectively. All these compounds were further evaluated for their inhibitory activities against VEGFR-2 protein. The results specified that among the tested compounds, 12d, 12e, 12k, 12l, 12p, 12q, 12t and 12u prominently suppressed VEGFR-2, with IC50 values of 310-920 nM in association to the positive control (210 nM). Angiogenesis inhibition was evident by tube formation assay in HUVECs and cell-invasion by transwell assay. The mechanism of cellular toxicity on MDA-MB-231 was found through depolarisation of mitochondrial membrane potential, increased ROS production and subsequent DNA damage resulting in apoptosis induction. Moreover, clonogenic and wound healing assays designated the inhibition of colony formation and cell migration by 12k in a dose-dependent manner. Molecular docking studies also shown that compound 12k capably intermingled with catalytically active residues GLU-885, ASP-1046 of the VEGFR-2 through hydrogen-bonding interactions.
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Dos Santos Maia M, Soares Rodrigues GC, Silva Cavalcanti AB, Scotti L, Scotti MT. Consensus Analyses in Molecular Docking Studies Applied to Medicinal Chemistry. Mini Rev Med Chem 2020; 20:1322-1340. [PMID: 32013847 DOI: 10.2174/1389557520666200204121129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023]
Abstract
The increasing number of computational studies in medicinal chemistry involving molecular docking has put the technique forward as promising in Computer-Aided Drug Design. Considering the main method in the virtual screening based on the structure, consensus analysis of docking has been applied in several studies to overcome limitations of algorithms of different programs and mainly to increase the reliability of the results and reduce the number of false positives. However, some consensus scoring strategies are difficult to apply and, in some cases, are not reliable due to the small number of datasets tested. Thus, for such a methodology to be successful, it is necessary to understand why, when and how to use consensus docking. Therefore, the present study aims to present different approaches to docking consensus, applications, and several scoring strategies that have been successful and can be applied in future studies.
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Affiliation(s)
- Mayara Dos Santos Maia
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Gabriela Cristina Soares Rodrigues
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Andreza Barbosa Silva Cavalcanti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Luciana Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Marcus Tullius Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
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Sharma K, Neshat N, Sharma S, Giri N, Srivastava A, Almalki F, Saifullah K, Alam MM, Shaquiquzzaman M, Akhter M. Identification of novel selective Mtb-DHFR inhibitors as antitubercular agents through structure-based computational techniques. Arch Pharm (Weinheim) 2019; 353:e1900287. [PMID: 31867798 DOI: 10.1002/ardp.201900287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/01/2019] [Accepted: 12/08/2019] [Indexed: 12/23/2022]
Abstract
Inhibition of dihydrofolate reductase from Mycobacterium tuberculosis-dihydrofolate reductase (Mtb-DHFR) has emerged as a promising approach for the treatment of tuberculosis. To identify novel Mtb-DHFR inhibitors, structure-based virtual screening (SBVS) of the Molecular Diversity Preservation International (MolMall) database was performed using Glide against the Mtb-DHFR and h-DHFR enzymes. On the basis of SBVS, receptor fit, drug-like filters, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis, 16 hits were selected and tested for their antitubercular activity against the H37 RV strain of M. tuberculosis. Five compounds showed promising activity with compounds 11436 and 15275 as the most potent hits with IC50 values of 0.65 and 12.51 μM, respectively, against the H37 RV strain of M. tuberculosis. The two compounds were further tested in the Mtb-DHFR and h-DHFR enzymatic assay for selectivity and were found to be three- to eight-fold selective towards Mtb-DHFR over h-DHFR with minimum inhibitory concentration values of 5.50, 73.89 µM and 42.00, 263.00 µM, respectively. In silico simulation studies also supported the stability of the protein-ligand complex formation. The present study demonstrates the successful utilization of in silico SBVS tools for the identification of novel and potential Mtb-DHFR inhibitors and compound 11436 ((2,4-dihydroxyphenyl)(3,4,5-trihydroxyphenyl)methanone) as a potential lead for the development of novel Mtb-DHFR inhibitors.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Nazia Neshat
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Shweta Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Namita Giri
- Department of Pharmaceutical Sciences, Ferris State University, Big Rapids, Michigan
| | - Apeksha Srivastava
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Faisal Almalki
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Khalid Saifullah
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Md Mumtaz Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | | | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India.,Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi, India
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An insight into the medicinal perspective of synthetic analogs of indole: A review. Eur J Med Chem 2019; 180:562-612. [PMID: 31344615 DOI: 10.1016/j.ejmech.2019.07.019] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/23/2019] [Accepted: 07/06/2019] [Indexed: 01/06/2023]
Abstract
Heterocycles occupy a salient place in chemistry due to their wide range of activity in the fields of drug design, photochemistry, agrochemicals, dyes, and so on. Amongst all, indole scaffold is considered as one of the most promising heterocycles found in natural and synthetic sources and has been shown to possess various biological activity, including anti-inflammatory, anti-HIV, antitubercular, antimalarial, anticonvulsant, antidiabetic, antihypertensive, analgesics, antidepressant, anticancer, antioxidant, antifungal, and antimicrobial, etc. All the reported indole molecules bind to multiple receptors with high affinity, thus expedite the research on the development of novel biologically active compounds through the various approach. In this review, we aimed to highlight synthetic and medicinal perspective on the development of indole-based analogs. In addition, structural activity relationship (SAR) study to correlate for their biological activity also discussed.
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Zampieri D, Cateni F, Moneghini M, Zacchigna M, Laurini E, Marson D, De Logu A, Sanna A, Mamolo MG. Imidazole and 1,2,4-Triazole-based Derivatives Gifted with Antitubercular Activity: Cytotoxicity and Computational Assessment. Curr Top Med Chem 2019; 19:620-632. [DOI: 10.2174/1568026619666190227183826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/13/2018] [Accepted: 08/31/2018] [Indexed: 11/22/2022]
Abstract
Background:Mycobacterium Tuberculosis (Mtb) is the causative pathogen of Tuberculosis (TB) and outbreaks are more common among immunosuppressed persons infected with HIV. The current treatment regimens are lengthy and toxic, yet the therapy has remained unchanged for many decades, so there is a need to find new structures with selective mechanism of action. Moreover, the increased incidence of severe disseminated infections produced by undiagnosed Multidrug-resistant (MDR), worsen clinical treatment and contribute the spread of the disease.Objective:The aim of our study was to evaluate the potential of imidazole and triazole moieties for antimycobacterial activity, by synthesizing some 1-(1-(aryl)-2-(2,6-dichlorophenyl)hydrazono)ethyl- 1H-imidazole and 1H-1,2,4-triazole derivatives 2a-l.Methods:The title compounds were obtained via classical organic synthesis. The antimicrobial activity was evaluated using the method of microdilution and the cytotoxicity assay was performed by MTT method.Results:The results indicated that the presence of both the imidazole ring and that of the 2,6- dichlorosubstituted phenyl moiety, is more relevant for inhibitory activity against Mtb than the triazole nucleus and the unsubstituted phenyl ring. Among the series, (E)-1-(2-(5-chlorothiophen-2-yl)-2-(2- (2,6-dichlorophenyl)hydrazono)ethyl)-1H-imidazole derivative 2f and (Z)-1-(2-([1,1’-biphenyl]-4-yl)- 2-(2-(2,6-dichlorophenyl)hydrazono)ethyl]-1H-imidazole derivatives 2e exhibited a promising antimycobacterial property and the latter also displayed a safe cytotoxic profile.Conclusion:The synthesized compounds were studied for their antitubercular activity. Among the series, the compounds 2e and 2f appeared to be the most promising agents and, according to the docking assessment, the compounds could be CYP51 inhibitors. These evidences could be useful for the future development of new antimycobacterial derivatives targeting CYP51 with more specificity for the mycobacterial cell enzyme.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemistry and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Francesca Cateni
- Department of Chemistry and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Mariarosa Moneghini
- Department of Chemistry and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Marina Zacchigna
- Department of Chemistry and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Via Valerio,10, University of Trieste, 34127 Trieste, Italy
| | - Domenico Marson
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Via Valerio,10, University of Trieste, 34127 Trieste, Italy
| | - Alessandro De Logu
- Department of Life and Enviromental Sciences, Via Porcell, 4, University of Cagliari, 09124 Cagliari, Italy
| | - Adriana Sanna
- Department of Life and Enviromental Sciences, Via Porcell, 4, University of Cagliari, 09124 Cagliari, Italy
| | - Maria G. Mamolo
- Department of Chemistry and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, 34127 Trieste, Italy
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Sharma K, Tanwar O, Deora GS, Ali S, Alam MM, Zaman MS, Krishna VS, Sriram D, Akhter M. Expansion of a novel lead targeting M. tuberculosis DHFR as antitubercular agents. Bioorg Med Chem 2019; 27:1421-1429. [PMID: 30827867 DOI: 10.1016/j.bmc.2019.02.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
A series of 1-(1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indol-3-yl)ethanone and ethyl 1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indole-3-carboxylate derivatives were designed based on bioisosteric replacement of previously reported antitubercular agent (IND-07). Twenty ligands were successfully synthesized and some of them were found to have good in vitro activity (MIC < 10 μM) against the H37Rv strain of Mycobacterium tuberculosis. Among these compounds, KC-08 and KC-11 inhibited Mtb-DHFR with 4- and 18-fold selectivity for Mtb-DHFR over h-DHFR, respectively. Compound KC-11 display acceptable ADME, and better pharmacokinetic profiles than IND-07. Docking studies were performed to predict the binding mode of the compounds within the active site of Mtb-DHFR and h-DHFR. The results of our study suggest that compound KC-11 may serve as a valuable lead for the design and development of selective inhibitors of Mtb-DHFR with potential therapeutic application in tuberculosis.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Omprakash Tanwar
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Girdhar Singh Deora
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - S Ali
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India; Bioinformatics Infrastructure Facility Lab, Jamia Hamdard, New Delhi 110062, India
| | - M M Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - M S Zaman
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India; Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India.
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Aleksandrov A, Myllykallio H. Advances and challenges in drug design against tuberculosis: application of in silico approaches. Expert Opin Drug Discov 2018; 14:35-46. [PMID: 30477360 DOI: 10.1080/17460441.2019.1550482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains the deadliest infectious disease in the world with one-third of the world's population thought to be infected. Over the years, TB mortality rate has been largely reduced; however, this progress has been threatened by the increasing appearance of multidrug-resistant Mtb. Considerable recent efforts have been undertaken to develop new generation antituberculosis drugs. Many of these attempts have relied on in silico approaches, which have emerged recently as powerful tools complementary to biochemical attempts. Areas covered: The authors review the status of pharmaceutical drug development against TB with a special emphasis on computational work. They focus on those studies that have been validated by in vitro and/or in vivo experiments, and thus, that can be considered as successful. The major goals of this review are to present target protein systems, to highlight how in silico efforts compliment experiments, and to aid future drug design endeavors. Expert opinion: Despite having access to all of the gene and protein sequences of Mtb, the search for new optimal treatments against this deadly pathogen are still ongoing. Together with the geometric growth of protein structural and sequence databases, computational methods have become a powerful technique accelerating the successful identification of new ligands.
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Affiliation(s)
- Alexey Aleksandrov
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
| | - Hannu Myllykallio
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
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