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Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024; 19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Affiliation(s)
- Christian S Carnero Canales
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- School of Pharmacy, biochemistry and biotechnology, Santa Maria Catholic University, Arequipa, Perú
| | - Aline Renata Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
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Duan SF, Song L, Guo HY, Deng H, Huang X, Shen QK, Quan ZS, Yin XM. Research status of indole-modified natural products. RSC Med Chem 2023; 14:2535-2563. [PMID: 38107170 PMCID: PMC10718587 DOI: 10.1039/d3md00560g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/19/2023] Open
Abstract
Indole is a heterocyclic compound formed by the fusion of a benzene ring and pyrrole ring, which has rich biological activity. Many indole-containing compounds have been sold on the market due to their excellent pharmacological activity. For example, vincristine and reserpine have been widely used in clinical practice. The diverse structures and biological activities of natural products provide abundant resources for the development of new drugs. Therefore, this review classifies natural products by structure, and summarizes the research progress of indole-containing natural product derivatives, their biological activities, structure-activity relationship and research mechanism which has been studied in the past 13 years, so as to provide a basis for the development of new drug development.
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Affiliation(s)
- Song-Fang Duan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Lei Song
- Yanbian University Hospital, Yanbian University Yanji 133002 People's Republic of China
| | - Hong-Yan Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Hao Deng
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Xing Huang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Qing-Kun Shen
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Zhe-Shan Quan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
| | - Xiu-Mei Yin
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University Yanji 133002 China +86 0433 243 6020 +86 0433 243 6019
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Desai NC, Khasiya AG, Jadeja DJ, Monapara JD, Jethawa AM, Dave BP, Sivan SK, Manga V, Mhaske PC, Chaudhary DR. Synthesis, Antifungal Ergosterol Inhibition, Antibiofilm Activities, and Molecular Docking on β-Tubulin and Sterol 14-Alpha Demethylase along with DFT-Based Quantum Mechanical Calculation of Pyrazole Containing Fused Pyridine-Pyrimidine Derivatives. ACS OMEGA 2023; 8:37781-37797. [PMID: 37867649 PMCID: PMC10586022 DOI: 10.1021/acsomega.3c01722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 10/24/2023]
Abstract
Multidrug-resistant fungal infections have become much more common in recent years, especially in immune-compromised patients. Therefore, researchers and pharmaceutical professionals have focused on the development of novel antifungal agents that can tackle the problem of resistance. In continuation to this, a novel series of pyrazole-bearing pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione derivatives (4a-4o) have been developed. These compounds have been screened against Candida albicans, Aspergillus niger, and Aspergillus clavatus. The synthesized compounds were characterized by well-known spectroscopic techniques, i.e., IR, 1H NMR, 13C NMR, and mass spectrometry. In vitro antifungal results revealed that compound 4n showed activity against C. albicans having MIC value of 200 μg/mL. To know the plausible mode of action, the active derivatives were screened for anti-biofilm and ergosterol biosynthesis inhibition activities. The compounds 4h, 4j, 4k, and 4n showed greater ergosterol biosynthesis inhibition than the control DMSO. To comprehend how molecules interact with the receptor, studies of molecular docking of 4k and 4n have been performed on the homology-modeled protein of β-tubulin. The molecular docking revealed that the active compounds 4h, 4j, 4k, 4l, and 4n interacting with the active site amino acid of sterol 14-alpha demethylase (PDB ID: 5v5z) indicate one of the possible modes of action of ergosterol inhibition activity. The synthesized compounds 4c, 4e, 4h, 4i, 4j, 4k, 4l, and 4n inhibited biofilm formation and possessed the potential for anti-biofilm activity. DFT-based quantum mechanical calculations were carried out to optimize, predict, and compare the vibration modes of the molecule 4a.
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Affiliation(s)
- Nisheeth C. Desai
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Ashvinkumar G. Khasiya
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Dharmpalsinh J. Jadeja
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Jahnvi D. Monapara
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Aratiba M. Jethawa
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Bharti P. Dave
- School
of Science, Indrashil University, Rajpur, Gujarat 382 740, India
| | - Sree Kanth Sivan
- Department
of Chemistry, University College for Women,
Osmania University, Koti, 500095 Hyderabad, India
| | - Vijjulatha Manga
- Department
of Chemistry, University College for Women,
Osmania University, Koti, 500095 Hyderabad, India
| | - Pravin C. Mhaske
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College, Tilak Road, Pune 411030, Maharashtra, India
| | - Doongar R. Chaudhary
- CSIR-Central
Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India
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Desai N, Jadeja D, Monapara J, Panda SK, Rana MK, Dave B. Design, synthesis, antimicrobial activity, DFT, and molecular docking studies of pyridine-pyrazole-based dihydro-1,3,4-oxadiazoles against various bacterial and fungal targets. J Biochem Mol Toxicol 2023; 37:e23377. [PMID: 37098749 DOI: 10.1002/jbt.23377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Antimicrobial resistance which is increasing at an alarming rate is a severe public health issue worldwide. Hence, the development of novel antibiotics is an urgent need as microbes have developed resistance against available antibiotics. In search of novel antimicrobial agents, a convenient route for the preparation of substituted 3-(1-phenyl-3-(p-tolyl)-1H-pyrazol-4-yl)-1-(2-phenyl-5-(pyridin-3-yl)-1,3,4-oxadiazol-3(2H)-yl)prop-2-en-1-ones (6a-6o) has been adopted by using pyridine-3-carbohydrazide and various aromatic aldehydes. The newly synthesized compounds were characterized by using various spectral techniques, for example, IR, 1 H NMR, 13 C NMR, and mass spectroscopy. Synthesized hybrids were studied for in vitro antimicrobial potency against various bacterial and fungal strains. Antibacterial results revealed that compounds 6e, 6h, 6i, 6l, and 6m were found to be most active against bacterial strains as they showed minimum inhibitory concentration (MIC) value of 62.5 μg/mL while compounds 6d, 6e, and 6h showed MIC value of 200 μg/mL against Candida albicans. The quantum parameters that relate to the bioavailability of the compounds were computed, followed by docking with different bacterial and fungal targets like sortase A, dihydrofolate reductase, thymidylate kinase, gyrase B, sterol 14-alpha demethylase. The experimental and computational results are in good agreement.
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Affiliation(s)
- Nisheeth Desai
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Dharmpalsinh Jadeja
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Jahnvi Monapara
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India
| | - Bharti Dave
- School of Science, Indrashil University, Kadi, Gujarat, India
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