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Arya PK, Mandal P, Barik K, Singh DV, Kumar A. Computational evaluation of phytochemicals targeting DNA topoisomerase I in Leishmania donovani: molecular docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2024; 42:8293-8306. [PMID: 37697722 DOI: 10.1080/07391102.2023.2256865] [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: 05/09/2023] [Accepted: 07/30/2023] [Indexed: 09/13/2023]
Abstract
DNA topoisomerase I (Topo I) is a ubiquitous enzyme that plays a crucial role in resolving the topological constraints of supercoiled DNA during various cellular activities, including repair, replication, recombination, transcription, and chromatin remodeling. Multiple studies have confirmed the essential role of Topo I in nucleic acid metabolism of Leishmania donovani, the kinetoplastid parasite responsible for visceral leishmaniasis or kala-azar. Inhibition of this enzyme has shown promise as a strategy for therapy against visceral leishmaniasis. However, current treatment options suffer from limitations related to effectiveness, cost, and side effects. To address these challenges, computational methods have been employed in this study to investigate the inhibition of Leishmania donovani DNA topoisomerase I (LdTopo I) by phytochemicals derived from Indian medicinal plants known for their anti-leishmanial activity. A library of phytochemicals and known inhibitors was assembled, and virtual screening based on docking binding affinities was conducted to identify potent phytochemical inhibitors. To assess the drug-likeness of the docked phytochemicals, their physicochemical properties were predicted. Additionally, molecular dynamics (MD) simulations were performed on the docked complexes for a duration of 100 ns to evaluate their stability, intermolecular interactions, and dynamic behavior. Among all the docked phytochemicals, three compounds, namely CID23266147 (withanolide N), CID5488537 (fagopyrine), and CID100947536 (isozeylanone), exhibited the highest inhibitory potential against LdTopo I. These findings hold promise for the development of novel inhibitors targeting LdTopo I, which could potentially lead to improved therapies for visceral leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pranabesh Mandal
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Krishnendu Barik
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Durg Vijay Singh
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Anil Kumar
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
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Singh R, Kashif M, Srivastava P, Manna PP. Recent Advances in Chemotherapeutics for Leishmaniasis: Importance of the Cellular Biochemistry of the Parasite and Its Molecular Interaction with the Host. Pathogens 2023; 12:pathogens12050706. [PMID: 37242374 DOI: 10.3390/pathogens12050706] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Leishmaniasis, a category 1 neglected protozoan disease caused by a kinetoplastid pathogen called Leishmania, is transmitted through dipteran insect vectors (phlebotomine, sand flies) in three main clinical forms: fatal visceral leishmaniasis, self-healing cutaneous leishmaniasis, and mucocutaneous leishmaniasis. Generic pentavalent antimonials have long been the drug of choice against leishmaniasis; however, their success is plagued with limitations such as drug resistance and severe side effects, which makes them redundant as frontline therapy for endemic visceral leishmaniasis. Alternative therapeutic regimens based on amphotericin B, miltefosine, and paromomycin have also been approved. Due to the unavailability of human vaccines, first-line chemotherapies such as pentavalent antimonials, pentamidine, and amphotericin B are the only options to treat infected individuals. The higher toxicity, adverse effects, and perceived cost of these pharmaceutics, coupled with the emergence of parasite resistance and disease relapse, makes it urgent to identify new, rationalized drug targets for the improvement in disease management and palliative care for patients. This has become an emergent need and more relevant due to the lack of information on validated molecular resistance markers for the monitoring and surveillance of changes in drug sensitivity and resistance. The present study reviewed the recent advances in chemotherapeutic regimens by targeting novel drugs using several strategies including bioinformatics to gain new insight into leishmaniasis. Leishmania has unique enzymes and biochemical pathways that are distinct from those of its mammalian hosts. In light of the limited number of available antileishmanial drugs, the identification of novel drug targets and studying the molecular and cellular aspects of these drugs in the parasite and its host is critical to design specific inhibitors targeting and controlling the parasite. The biochemical characterization of unique Leishmania-specific enzymes can be used as tools to read through possible drug targets. In this review, we discuss relevant metabolic pathways and novel drugs that are unique, essential, and linked to the survival of the parasite based on bioinformatics and cellular and biochemical analyses.
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Affiliation(s)
- Ranjeet Singh
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mohammad Kashif
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prateek Srivastava
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Partha Pratim Manna
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Lamba S, Roy A. Demystifying the potential of inhibitors targeting DNA topoisomerases in unicellular protozoan parasites. Drug Discov Today 2023; 28:103574. [PMID: 37003515 DOI: 10.1016/j.drudis.2023.103574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/09/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023]
Abstract
DNA topoisomerases are a group of enzymes omnipresent in all organisms. They maintain the DNA topology during replication, repair, recombination, and transcription. However, the structure of topoisomerase in protozoan parasites differs significantly from that of human topoisomerases; thus, this enzyme acts as a crucial target in drug development against parasitic diseases. Although the therapeutic potential of drugs targeting the parasitic topoisomerase is well known, to manage the shortcomings of currently available therapeutics and the emergence of drug resistance, the discovery of novel antiparasitic molecules is an urgent need. In this review, we describe various investigational and repurposed topoisomerase inhibitors developed against protozoan parasites over the past few years. Teaser: Fatal parasitic diseases are an increasing cause for concern; here, we provide a compilation of different inhibitors targeting DNA topoisomerases, enzymes that are essential for, and unique to, protozoan parasites; therefore, inhibitors are efficient and have few adverse effects.
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Affiliation(s)
- Swati Lamba
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Amit Roy
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India.
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Albino SL, da Silva Moura WC, dos Reis MML, Sousa GLS, da Silva PR, de Oliveira MGC, Borges TKDS, Albuquerque LFF, de Almeida SMV, de Lima MDCA, Kuckelhaus SAS, Nascimento IJDS, Junior FJBM, da Silva TG, de Moura RO. ACW-02 an Acridine Triazolidine Derivative Presents Antileishmanial Activity Mediated by DNA Interaction and Immunomodulation. Pharmaceuticals (Basel) 2023; 16:204. [PMID: 37259353 PMCID: PMC9967605 DOI: 10.3390/ph16020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/11/2024] Open
Abstract
The present study proposed the synthesis of a novel acridine derivative not yet described in the literature, chemical characterization by NMR, MS, and IR, followed by investigations of its antileishmanial potential. In vitro assays were performed to assess its antileishmanial activity against L. amazonensis strains and cytotoxicity against macrophages through MTT assay and annexin V-FITC/PI, and the ability to perform an immunomodulatory action using CBA. To investigate possible molecular targets, its interaction with DNA in vitro and in silico targets were evaluated. As results, the compound showed good antileishmanial activity, with IC50 of 6.57 (amastigotes) and 94.97 (promastigotes) µg mL-1, associated with non-cytotoxicity to macrophages (CC50 > 256.00 µg mL-1). When assessed by flow cytometry, 99.8% of macrophages remained viable. The compound induced an antileishmanial effect in infected macrophages and altered TNF-α, IL-10 and IL-6 expression, suggesting a slight immunomodulatory activity. DNA assay showed an interaction with the minor grooves due to the hyperchromic effect of 47.53% and Kb 1.17 × 106 M-1, and was sustained by docking studies. Molecular dynamics simulations and MM-PBSA calculations propose cysteine protease B as a possible target. Therefore, this study demonstrates that the new compound is a promising molecule and contributes as a model for future works.
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Affiliation(s)
- Sonaly Lima Albino
- Programa de Pós Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Willian Charles da Silva Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Malu Maria Lucas dos Reis
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Gleyton Leonel Silva Sousa
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, Brazil
| | - Pablo Rayff da Silva
- Programa de Pós Graduação em Produtos Naturais, Sintéticos e Bioativos, Universidade Federal da Paraiba, João Pessoa 58051-900, Brazil
| | | | - Tatiana Karla dos Santos Borges
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | - Lucas Fraga Friaça Albuquerque
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica, Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Selma Aparecida Souza Kuckelhaus
- Área de Morfologia, Faculdade de Medicina—UnB, Universidade de Brasília, Campus Darcy Ribeiro/Asa Norte, Brasília 70910-900, Brazil
| | - Igor José dos Santos Nascimento
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | | | | | - Ricardo Olímpio de Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
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Goel N, Gupta VK, Garg A, Bhoumik A, Biswas R, Natarajan R, Majumder HK, Jaisankar P. Holanamine, a Steroidal Alkaloid from the Bark of Holarrhena pubescens Wall. ex G. Don Inhibits the Growth of Leishmania donovani by Targeting DNA Topoisomerase 1B. ACS Infect Dis 2023; 9:162-177. [PMID: 36417798 DOI: 10.1021/acsinfecdis.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Leishmaniasis is a group of neglected tropical diseases (NTDs) caused by about 20 species of obligate intracellular protozoan parasites of the genus Leishmania, which occurs in cutaneous, mucocutaneous, and visceral forms. Many researchers have sought to utilize natural products for novel and effective treatments to combat many infectious diseases, including leishmaniasis. Holarrhena pubescens Wall. ex G. Don (Apocynaceae) bark is a rich source of bioactive steroidal alkaloids. The total alkaloidal extract (IC50 6.12 ± 0.117 μg/mL), and the isolated alkaloid, holanamine, showed significant antileishmanial activity (IC50 2.66 ± 0.112 μM against AG83 and 3.80 ± 0.126 μM against BHU-575) against the Leishmania donovani parasite, better than miltefosine (IC50 19.61 ± 0.093 μM against AG83 and 23.20 ± 0.094 μM against BHU-575). Holanamine inhibited the L. donovani topoisomerase 1B (LdToP1B) in a non-competitive manner (IC50 2.81 ± 0.105 μM), indicating that it interacts with the free enzyme and enzyme-DNA complex without inhibiting human topoisomerase. Hydrogen bonding and hydrophobic interactions of holanamine with the N-terminal and hinge region of the large subunit of LTop1B is responsible for its potent antileishmanial activity, as shown by docking studies. Treatment with holanamine causes apoptotic-like cell death by generating cellular and mitochondrial reactive oxygen species, disrupting the mitochondrial membrane potential and inducing ultrastructural alterations in the promastigotes. Holanamine effectively clears intracellular amastigotes but minimally affects host macrophages with no significant cytotoxicity in HEK 293 and L929 cell lines. Thus, our studies show that holanamine can further be used to develop effective antileishmanial agents against evolving drug-resistant parasites.
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Affiliation(s)
- Narender Goel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala Main Road, Kolkata700054, India.,Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Vivek Kumar Gupta
- Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Aakriti Garg
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala Main Road, Kolkata700054, India
| | - Arpita Bhoumik
- Laboratory of Molecular Parasitology, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Raju Biswas
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ramalingam Natarajan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Parasuraman Jaisankar
- Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
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6
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Shi D, Pang Q, Qin Q, Yao X, Yao X, Yu Y. Discovery of novel anti-tumor compounds targeting PARP-1 with induction of autophagy through in silico and in vitro screening. Front Pharmacol 2022; 13:1026306. [PMID: 36353483 PMCID: PMC9638114 DOI: 10.3389/fphar.2022.1026306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP-1) is a critical enzyme involved in DNA damage repair and recombination, and shows great potential for drug development in the treatment of cancers with defective DNA repair. The anti-tumor activities of PARP-1 inhibitors are regulated by both inhibition activities and allosteric mechanisms of PARP-1, and may also be involved in an autophagy-mediated process. Screening PARP-1 inhibitors with potential allosteric mechanisms and induced autophagy process could achieve elevated potency toward cancer cell killing. In this study, we tried to discover novel anti-tumor compounds targeting PARP-1 by computer simulations and in vitro screening. In order to filter PARP-1 inhibitors that could affect the folding state of the helix domain (HD) on PARP-1, the free energy contribution of key residues on HD were systematically analyzed using the ligand-binding crystal structures and integrated into in silico screening workflow for the selection of 20 pick-up compounds. Four compounds (Chemdiv codes: 8012-0567, 8018-6529, 8018-7168, 8018-7603) were proved with above 40% inhibitory ratio targeting PARP-1 under 20 μM, and further performed binding mode prediction and dynamic effect evaluation by molecular dynamics simulation. Further in vitro assays showed that compounds 8018-6529 and 8018-7168 could inhibit the growth of the human colorectal cancer cell (HCT-116) with IC50 values of 4.30 and 9.29 μM and were accompanied with an induced autophagy process. Taken together, we discover two novel anti-tumor compounds that target PARP-1 with an induced autophagy process and provide potential hit compounds for the anti-cancer drug development.
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Affiliation(s)
- Danfeng Shi
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Yang Yu, ; Danfeng Shi,
| | - Qianqian Pang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Qianyu Qin
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xinsheng Yao
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Yang Yu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Yang Yu, ; Danfeng Shi,
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Borkar MR, Martis EAF, Nandan S, Patil RH, Shelar A, Iyer KR, Raikuvar K, Desle D, Coutinho EC. Identification of potential antileishmanial 1,3-disubstituted-4-hydroxy-6-methylpyridin-2(1H)-ones, in vitro metabolic stability, cytotoxicity and molecular modeling studies. Chem Biol Interact 2022; 351:109758. [PMID: 34826397 DOI: 10.1016/j.cbi.2021.109758] [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: 08/14/2021] [Revised: 11/10/2021] [Accepted: 11/21/2021] [Indexed: 11/18/2022]
Abstract
We report the synthesis and in vitro evaluation of 1,3-disubstituted-4-hydroxy-6-methylpyridin-2(1H)-one derivatives against Leishmania donovani. Amongst the compound library synthesized, molecules 3d, 3f, 3h, 3i, 3l, and 3m demonstrated substantial dose-dependent killing of the promastigotes. Their IC50 values range from 55.0 to 77.0 μg/ml, with 3m (IC50 55.75 μg/ml) being equipotent with amphotericin B (IC50 50.0 μg/ml, used as standard). The most active compound 3m, is metabolically stable in rat liver microsomes. Furthermore, the molecules are highly specific against leishmania as shown by their weak antibacterial and antifungal activity. In vitro cytotoxicity studies show the compounds lack any cytotoxicity. Furthermore, molecular modeling studies show plausibility of binding to Leishmania donovani topoisomerase 1 (LdTop1). Structure activity relationships reveal bulky substitutions on the pyridone nitrogen are well-tolerated, and such compounds have better binding affinity. Intramolecular hydrogen bonds confer some rigidity to the molecules, rendering a degree of planarity akin to topotecan. Taken together, we emphasis the merits of molecules possessing the 1,3-disubstituted-4-hydroxy-6-methylpyridin-2(1H)-one skeleton as potential antileishmanial agents warranting further investigation.
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Affiliation(s)
- Maheshkumar R Borkar
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India; Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India.
| | - Elvis A F Martis
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India
| | - Santosh Nandan
- Ambernath Organics Pvt. Ltd., 222, The Summit Business Bay, Andheri (E), Mumbai, 400 093, India
| | - Rajendra H Patil
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411 007, India
| | - Amruta Shelar
- Department of Technology, Savitribai Phule Pune University, Pune, 4110 007, India
| | - Krishna R Iyer
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India
| | - Kavita Raikuvar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India
| | - Deepali Desle
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India
| | - Evans C Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Sunder Nagar, Kalina, Santacruz (E), Mumbai, 400 098, India
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The ultimate fate determinants of drug induced cell-death mechanisms in Trypanosomatids. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 15:81-91. [PMID: 33601284 PMCID: PMC7900639 DOI: 10.1016/j.ijpddr.2021.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
Chemotherapy constitutes a major part of modern-day therapy for infectious and chronic diseases. A drug is said to be effective if it can inhibit its target, induce stress, and thereby trigger an array of cell death pathways in the form of programmed cell death, autophagy, necrosis, etc. Chemotherapy is the only treatment choice against trypanosomatid diseases like Leishmaniasis, Chagas disease, and sleeping sickness. Anti-trypanosomatid drugs can induce various cell death phenotypes depending upon the drug dose and growth stage of the parasites. The mechanisms and pathways triggering cell death in Trypanosomatids serve to help identify potential targets for the development of effective anti-trypanosomatids. Studies show that the key proteins involved in cell death of trypanosomatids are metacaspases, Endonuclease G, Apoptosis-Inducing Factor, cysteine proteases, serine proteases, antioxidant systems, etc. Unlike higher eukaryotes, these organisms either lack the complete set of effectors involved in cell death pathways, or are yet to be deciphered. A detailed summary of the existing knowledge of different drug-induced cell death pathways would help identify the lacuna in each of these pathways and therefore open new avenues for research and thereby new therapeutic targets to explore. The cell death pathway associated complexities in metazoans are absent in trypanosomatids; hence this summary can also help understand the trigger points as well as cross-talk between these pathways. Here we provide an in-depth overview of the existing knowledge of these drug-induced trypanosomatid cell death pathways, describe their associated physiological changes, and suggest potential interconnections amongst them.
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Raj S, Sasidharan S, Balaji SN, Saudagar P. An overview of biochemically characterized drug targets in metabolic pathways of Leishmania parasite. Parasitol Res 2020; 119:2025-2037. [DOI: 10.1007/s00436-020-06736-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022]
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Reguera RM, Elmahallawy EK, García-Estrada C, Carbajo-Andrés R, Balaña-Fouce R. DNA Topoisomerases of Leishmania Parasites; Druggable Targets for Drug Discovery. Curr Med Chem 2019; 26:5900-5923. [DOI: 10.2174/0929867325666180518074959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
DNA topoisomerases (Top) are a group of isomerase enzymes responsible for controlling the topological problems caused by DNA double helix in the cell during the processes of replication, transcription and recombination. Interestingly, these enzymes have been known since long to be key molecular machines in several cellular processes through overwinding or underwinding of DNA in all living organisms. Leishmania, a trypanosomatid parasite responsible for causing fatal diseases mostly in impoverished populations of low-income countries, has a set of six classes of Top enzymes. These are placed in the nucleus and the single mitochondrion and can be deadly targets of suitable drugs. Given the fact that there are clear differences in structure and expression between parasite and host enzymes, numerous studies have reported the therapeutic potential of Top inhibitors as antileishmanial drugs. In this regard, numerous compounds have been described as Top type IB and Top type II inhibitors in Leishmania parasites, such as camptothecin derivatives, indenoisoquinolines, indeno-1,5- naphthyridines, fluoroquinolones, anthracyclines and podophyllotoxins. The aim of this review is to highlight several facts about Top and Top inhibitors as potential antileishmanial drugs, which may represent a promising strategy for the control of this disease of public health importance.
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Affiliation(s)
- Rosa M. Reguera
- Department of Biomedical Sciences, University of Leon (ULE), Leon, Spain
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Cinelli MA. Topoisomerase 1B poisons: Over a half-century of drug leads, clinical candidates, and serendipitous discoveries. Med Res Rev 2018; 39:1294-1337. [PMID: 30456874 DOI: 10.1002/med.21546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022]
Abstract
Topoisomerases are DNA processing enzymes that relieve supercoiling (torsional strain) in DNA, are necessary for normal cellular division, and act by nicking (and then religating) DNA strands. Type 1B topoisomerase (Top1) is overexpressed in certain tumors, and the enzyme has been extensively investigated as a target for cancer chemotherapy. Various chemical agents can act as "poisons" of the enzyme's religation step, leading to Top1-DNA lesions, DNA breakage, and eventual cellular death. In this review, agents that poison Top1 (and have thus been investigated for their anticancer properties) are surveyed, including natural products (such as camptothecins and indolocarbazoles), semisynthetic camptothecin and luotonin derivatives, and synthetic compounds (such as benzonaphthyridines, aromathecins, and indenoisoquinolines), as well as targeted therapies and conjugates. Top1 has also been investigated as a therapeutic target in certain viral and parasitic infections, as well as autoimmune, inflammatory, and neurological disorders, and a summary of literature describing alternative indications is also provided. This review should provide both a reference for the medicinal chemist and potentially offer clues to aid in the development of new Top1 poisons.
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Affiliation(s)
- Maris A Cinelli
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
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12
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Ferreira LLG, Andricopulo AD. Chemoinformatics Strategies for Leishmaniasis Drug Discovery. Front Pharmacol 2018; 9:1278. [PMID: 30443215 PMCID: PMC6221941 DOI: 10.3389/fphar.2018.01278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/18/2018] [Indexed: 12/15/2022] Open
Abstract
Leishmaniasis is a fatal neglected tropical disease (NTD) that is caused by more than 20 species of Leishmania parasites. The disease kills approximately 20,000 people each year and more than 1 billion are susceptible to infection. Although counting on a few compounds, the therapeutic arsenal faces some drawbacks such as drug resistance, toxicity issues, high treatment costs, and accessibility problems, which highlight the need for novel treatment options. Worldwide efforts have been made to that aim and, as well as in other therapeutic areas, chemoinformatics have contributed significantly to leishmaniasis drug discovery. Breakthrough advances in the comprehension of the parasites’ molecular biology have enabled the design of high-affinity ligands for a number of macromolecular targets. In addition, the use of chemoinformatics has allowed highly accurate predictions of biological activity and physicochemical and pharmacokinetics properties of novel antileishmanial compounds. This review puts into perspective the current context of leishmaniasis drug discovery and focuses on the use of chemoinformatics to develop better therapies for this life-threatening condition.
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Affiliation(s)
- Leonardo L G Ferreira
- Laboratory of Medicinal and Computational Chemistry, Center for Research and Innovation in Biodiversity and Drug Discovery, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Adriano D Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Center for Research and Innovation in Biodiversity and Drug Discovery, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
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13
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Salfeena CF, Jalaja R, Davis R, Suresh E, Somappa SB. Synthesis of 1,2,4-Trisubstituted-(1 H)-imidazoles through Cu(OTf) 2-/I 2-Catalyzed C-C Bond Cleavage of Chalcones and Benzylamines. ACS OMEGA 2018; 3:8074-8082. [PMID: 31458944 PMCID: PMC6644843 DOI: 10.1021/acsomega.8b01017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 06/10/2023]
Abstract
1,2,4-Trisubstituted-(1H)-imidazoles have been synthesized by the Cu(OTf)2- and I2-catalyzed unusual C-C bond cleavage of chalcones and benzylamines. After the α,β-unsaturated C-C bond cleavage, the β-portion is eliminated from the reaction. Various aryl- and heteroaryl-substituted chalcones and benzylamines were well tolerated in this unusual transformation to yield the trisubstituted-(1H)-imidazoles.
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Affiliation(s)
- Chettiyan
Thodi F. Salfeena
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695
019, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Thiruvananthapuram 695 019, India
| | - Renjitha Jalaja
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695
019, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Thiruvananthapuram 695 019, India
| | - Rincy Davis
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695
019, India
| | - Eringathodi Suresh
- Analytical
Department and Centralized Instrument Facility, CSIR-CSMCRI, Bhavnagar 364 002, India
| | - Sasidhar B. Somappa
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695
019, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Thiruvananthapuram 695 019, India
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14
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Xin LT, Liu L, Shao CL, Yu RL, Chen FL, Yue SJ, Wang M, Guo ZL, Fan YC, Guan HS, Wang CY. Discovery of DNA Topoisomerase I Inhibitors with Low-Cytotoxicity Based on Virtual Screening from Natural Products. Mar Drugs 2017; 15:md15070217. [PMID: 28698495 PMCID: PMC5532659 DOI: 10.3390/md15070217] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 01/17/2023] Open
Abstract
Currently, DNA topoisomerase I (Topo I) inhibitors constitute a family of antitumor agents with demonstrated clinical effects on human malignancies. However, the clinical uses of these agents have been greatly limited due to their severe toxic effects. Therefore, it is urgent to find and develop novel low toxic Topo I inhibitors. In recent years, during our ongoing research on natural antitumor products, a collection of low cytotoxic or non-cytotoxic compounds with various structures were identified from marine invertebrates, plants, and their symbiotic microorganisms. In the present study, new Topo I inhibitors were discovered from low cytotoxic and non-cytotoxic natural products by virtual screening with docking simulations in combination with bioassay test. In total, eight potent Topo I inhibitors were found from 138 low cytotoxic or non-cytotoxic compounds from coral-derived fungi and plants. All of these Topo I inhibitors demonstrated activities against Topo I-mediated relaxation of supercoiled DNA at the concentrations of 5–100 µM. Notably, the flavonoids showed higher Topo I inhibitory activities than other compounds. These newly discovered Topo I inhibitors exhibited structurally diverse and could be considered as a good starting point for the development of new antitumor lead compounds.
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Affiliation(s)
- Lan-Ting Xin
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Ri-Lei Yu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Fang-Ling Chen
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Shi-Jun Yue
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Mei Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Zhong-Long Guo
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Ya-Chu Fan
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Hua-Shi Guan
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Yao TT, Xiao DX, Li ZS, Cheng JL, Fang SW, Du YJ, Zhao JH, Dong XW, Zhu GN. Design, Synthesis, and Fungicidal Evaluation of Novel Pyrazole-furan and Pyrazole-pyrrole Carboxamide as Succinate Dehydrogenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5397-5403. [PMID: 28616975 DOI: 10.1021/acs.jafc.7b01251] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The identification of novel succinate dehydrogenase (SDH) inhibitors represents one of the most attractive directions in the field of fungicide research and development. During our continuous efforts to pursue inhibitors belonging to this class, some structurally novel pyrazole-furan carboxamide and pyrazole-pyrrole carboxamide derivatives have been discovered via the introduction of scaffold hopping and bioisosterism to compound 1, a remarkably potent lead obtained by pharmacophore-based virtual screening. As a result of the evaluation against three destructive fungi, including Sclerotinia sclerotiorum, Rhizoctonia solani, and Pyricularia grisea, a majority of them displayed potent fungicidal activities. In particular, compounds 12I-i, 12III-f, and 12III-o exhibited excellent fungicidal activity against S. sclerotiorum and R. solani comparable to that of commercial SDHI thifluzamide and 1.
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Affiliation(s)
- Ting-Ting Yao
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Dou-Xin Xiao
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Zhong-Shan Li
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Jing-Li Cheng
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Shao-Wei Fang
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Yong-Jun Du
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Jin-Hao Zhao
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
| | - Xiao-Wu Dong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310058, P. R. China
| | - Guo-Nian Zhu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou 310029, P. R. China
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16
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Liu R, Li X, Lam KS. Combinatorial chemistry in drug discovery. Curr Opin Chem Biol 2017; 38:117-126. [PMID: 28494316 PMCID: PMC5645069 DOI: 10.1016/j.cbpa.2017.03.017] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023]
Abstract
Several combinatorial methods have been developed to create focused or diverse chemical libraries with a wide range of linear or macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. Each combinatorial approach has its own unique high-throughput screening and encoding strategy. In this article, we provide a brief overview of combinatorial chemistry in drug discovery with emphasis on recently developed new technologies for design, synthesis, screening and decoding of combinatorial library. Examples of successful application of combinatorial chemistry in hit discovery and lead optimization are given. The limitations and strengths of combinatorial chemistry are also briefly discussed. We are now in a better position to truly leverage the power of combinatorial technologies for the discovery and development of next-generation drugs.
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Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA.
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