1
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Mahanta PJ, Lhouvum K. Plasmodium falciparum proteases as new drug targets with special focus on metalloproteases. Mol Biochem Parasitol 2024; 258:111617. [PMID: 38554736 DOI: 10.1016/j.molbiopara.2024.111617] [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: 10/17/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Malaria poses a significant global health threat particularly due to the prevalence of Plasmodium falciparum infection. With the emergence of parasite resistance to existing drugs including the recently discovered artemisinin, ongoing research seeks novel therapeutic avenues within the malaria parasite. Proteases are promising drug targets due to their essential roles in parasite biology, including hemoglobin digestion, merozoite invasion, and egress. While exploring the genomic landscape of Plasmodium falciparum, it has been revealed that there are 92 predicted proteases, with only approximately 14 of them having been characterized. These proteases are further distributed among 26 families grouped into five clans: aspartic proteases, cysteine proteases, metalloproteases, serine proteases, and threonine proteases. Focus on metalloprotease class shows further role in organelle processing for mitochondria and apicoplasts suggesting the potential of metalloproteases as viable drug targets. Holistic understanding of the parasite intricate life cycle and identification of potential drug targets are essential for developing effective therapeutic strategies against malaria and mitigating its devastating global impact.
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Affiliation(s)
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
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2
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Madhav H, Reddy GS, Rizvi Z, Jameel E, Patel TS, Rahman A, Yadav V, Fatima S, Heyat F, Pal K, Minju-Op A, Subbarao N, Bhattacharjee S, Dixit BC, Sijwali PS, Hoda N. Reinvestigation of diphenylmethylpiperazine analogues of pyrazine as new class of Plasmodial cysteine protease inhibitors for the treatment of malaria. RSC Med Chem 2024; 15:1022-1037. [PMID: 38516592 PMCID: PMC10953474 DOI: 10.1039/d3md00490b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/19/2023] [Indexed: 03/23/2024] Open
Abstract
Malaria eradication is still a global challenge due to the lack of a broadly effective vaccine and the emergence of drug resistance to most of the currently available drugs as part of the mainline artemisinin-based combination therapy. A variety of experimental approaches are quite successful in identifying and synthesizing new promising pharmacophore hybrids with distinct mechanisms of action. Based on our recent findings, the current study demonstrates the reinvestigation of a series of diphenylmethylpiperazine and pyrazine-derived molecular hybrids. Pyrazine-derived molecular hybrids were screened to investigate the antiplasmodial activity on drug-susceptible Pf3D7 and drug-resistant PfW2 strains. The selected compounds were shown to be potent dual inhibitors of cysteine protease PfFP2 and PfFP3. Time-course parasitic development study demonstrated that compounds were able to arrest the growth of the parasite at the early trophozoite stage. The compounds did not show hemolysis of red blood cells and showed selectivity to the parasite compared with the mammalian Vero and A5489 cell lines. The study underlined HR5 and HR15 as a new class of Plasmodial falcipain inhibitors with an IC50 of 6.2 μM and 5.9 μM for PfFP2 and 6.8 μM and 6.4 μM for PfFP3, respectively. Both compounds have antimalarial efficacy with IC50 values of 3.05 μM and 2.80 μM for the Pf3D7 strain, and 4.35 μM and 3.39 μM for the PfW2 strain, respectively. Further structural optimization may turn them into potential Plasmodial falcipain inhibitors for malaria therapeutics.
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Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - G Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Ehtesham Jameel
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Tarosh S Patel
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University Vallabh Vidyanagar-388120 Gujarat India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University New Delhi-110067 India
| | - Vikas Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Sadaf Fatima
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Fatima Heyat
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Kavita Pal
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Amisha Minju-Op
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University New Delhi-110067 India
| | - Bharat C Dixit
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
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3
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Nath M, Bhowmik D, Saha S, Nandi R, Kumar D. Identification of potential inhibitor against Leishmania donovani mitochondrial DNA primase through in-silico and in vitro drug repurposing approaches. Sci Rep 2024; 14:3246. [PMID: 38332162 PMCID: PMC10853515 DOI: 10.1038/s41598-024-53316-5] [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: 10/07/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Leishmania donovani is the causal organism of leishmaniasis with critical health implications affecting about 12 million people around the globe. Due to less efficacy, adverse side effects, and resistance, the available therapeutic molecules fail to control leishmaniasis. The mitochondrial primase of Leishmania donovani (LdmtPRI1) is a vital cog in the DNA replication mechanism, as the enzyme initiates the replication of the mitochondrial genome of Leishmania donovani. Hence, we target this protein as a probable drug target against leishmaniasis. The de-novo approach enabled computational prediction of the three-dimensional structure of LdmtPRI1, and its active sites were identified. Ligands from commercially available drug compounds were selected and docked against LdmtPRI1. The compounds were chosen for pharmacokinetic study and molecular dynamics simulation based on their binding energies and protein interactions. The LdmtPRI1 gene was cloned, overexpressed, and purified, and a primase activity assay was performed. The selected compounds were verified experimentally by the parasite and primase inhibition assay. Capecitabine was observed to be effective against the promastigote form of Leishmania donovani, as well as inhibiting primase activity. This study's findings suggest capecitabine might be a potential anti-leishmanial drug candidate after adequate further studies.
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Affiliation(s)
- Mitul Nath
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Deep Bhowmik
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Satabdi Saha
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Rajat Nandi
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
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4
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Madhav H, Patel TS, Rizvi Z, Reddy GS, Rahman A, Rahman MA, Ahmedi S, Fatima S, Saxena K, Manzoor N, Bhattacharjee S, Dixit BC, Sijwali PS, Hoda N. Development of diphenylmethylpiperazine hybrids of chloroquinoline and triazolopyrimidine using Petasis reaction as new cysteine proteases inhibitors for malaria therapeutics. Eur J Med Chem 2023; 258:115564. [PMID: 37321109 DOI: 10.1016/j.ejmech.2023.115564] [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: 05/14/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/17/2023]
Abstract
Malaria is a widespread infectious disease, causing nearly 247 million cases in 2021. The absence of a broadly effective vaccine and rapidly decreasing effectiveness of most of the currently used antimalarials are the major challenges to malaria eradication efforts. To design and develop novel antimalarials, we synthesized a series of 4,7-dichloroquinoline and methyltriazolopyrimidine analogues using a multi-component Petasis reaction. The synthesized molecules (11-31) were screened for in-vitro antimalarial activity against drug-sensitive and drug-resistant strains of Plasmodium falciparum with an IC50 value of 0.53 μM. The selected compounds were screened to evaluate in-vitro and in-silico enzyme inhibition efficacy against two cysteine proteases, PfFP2 and PfFP3. The compounds 15 and 17 inhibited PfFP2 with an IC50 = 3.5 and 4.8 μM, respectively and PfFP3 with an IC50 = 4.9 and 4.7 μM, respectively. Compounds 15 and 17 were found equipotent against the Pf3D7 strain with an IC50 value of 0.74 μM, whereas both were displayed IC50 values of 1.05 μM and 1.24 μM for the PfW2 strain, respectively. Investigation of effect of compounds on parasite development demonstrated that compounds were able to arrest the growth of the parasites at trophozoite stage. The selected compounds were screened for in-vitro cytotoxicity against mammalian lines and human red-blood-cell (RBC), which demonstrated no significant cytotoxicity associated with the molecules. In addition, in silico ADME prediction and physiochemical properties supported the drug-likeness of the synthesized molecules. Thus, the results highlighted the diphenylmethylpiperazine group cast on 4,7-dichloroquinoline and methyltriazolopyrimidine using Petasis reaction may serve as models for the development of new antimalarial agents.
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Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Tarosh S Patel
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University, Vallabh Vidyanagar, 388 120, Gujarat, India
| | - Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - G Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Md Ataur Rahman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Saiema Ahmedi
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sadaf Fatima
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Kanika Saxena
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Nikhat Manzoor
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Bharat C Dixit
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University, Vallabh Vidyanagar, 388 120, Gujarat, India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India.
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5
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Tukur A, Habila JD, Ayo RGO, Iyun ORA. Synthesis, characterization and antibiotic evaluation of some novel (E)-3-(4-diphenylamino)phenyl)-1-(4′-fluorophenyl)prop-2-en-1-one chalcones and their analogues. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The increase in resistance of pathogenic organisms to the available chemotherapeutic agents are critical challenges in drug design and development, motivating researchers to look for novel compounds that can combat multidrug-resistant organisms. Recently, chalcones have been proved to be attractive moieties in drug discovery.
Results
Eight novel triphenylamine chalcones with different substitution patterns were successfully synthesized via the conventional Claisen–Schmidt condensation reaction in an alkaline medium at room temperature, and recrystallized using ethanol, the percentage yield of the compounds were between 30 and 92%. The structures of the synthesized chalcones were successfully characterized and confirmed using FT-IR, NMR spectroscopic and GC–MS spectrometric techniques.
Conclusions
The results of the biological studies showed that all the synthesized chalcones possess remarkable activities against the tested microbes, by showing a significant zone of inhibitions relative to that of the standard drugs used. The investigation revealed that 1b showed highest ZOI (30 mm), lowest MIC (12.5 µg/ml) and MBC/MFC (50 µg/ml) on Aspergillus niger. Therefore, displayed better antifungal potential as compared to the rest of the compounds, and can be a potential antifungal drug candidate.
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Uddin A, Gupta S, Mohammad T, Shahi D, Hussain A, Alajmi MF, El-Seedi HR, Hassan I, Singh S, Abid M. Target-Based Virtual Screening of Natural Compounds Identifies a Potent Antimalarial With Selective Falcipain-2 Inhibitory Activity. Front Pharmacol 2022; 13:850176. [PMID: 35462917 PMCID: PMC9020225 DOI: 10.3389/fphar.2022.850176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
We employed a comprehensive approach of target-based virtual high-throughput screening to find potential hits from the ZINC database of natural compounds against cysteine proteases falcipain-2 and falcipain-3 (FP2 and FP3). Molecular docking studies showed the initial hits showing high binding affinity and specificity toward FP2 were selected. Furthermore, the enzyme inhibition and surface plasmon resonance assays were performed which resulted in a compound ZINC12900664 (ST72) with potent inhibitory effects on purified FP2. ST72 exhibited strong growth inhibition of chloroquine-sensitive (3D7; EC50 = 2.8 µM) and chloroquine-resistant (RKL-9; EC50 = 6.7 µM) strains of Plasmodium falciparum. Stage-specific inhibition assays revealed a delayed and growth defect during parasite growth and development in parasites treated with ST72. Furthermore, ST72 significantly reduced parasite load and increased host survival in a murine model infected with Plasmodium berghei ANKA. No Evans blue staining in ST72 treatment indicated that ST72 mediated protection of blood–brain barrier integrity in mice infected with P. berghei. ST72 did not show any significant hemolysis or cytotoxicity against human HepG2 cells suggesting a good safety profile. Importantly, ST72 with CQ resulted in improved growth inhibitory activity than individual drugs in both in vitro and in vivo studies.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonal Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Diksha Shahi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hesham R. El-Seedi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
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7
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Irudaya Jothi A, Rajarathinam C, Arun Viveke A, Bosco Paul MW. Substituent effects on the mesogenic benzylidenes of 4-methylaniline: Synthesis, characterization, DFT, NLO, photophysical, molecular docking, and antibacterial studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Gouda MA, Al‐Ghorbani M, Al‐Zaqri N. Synthesis and cytotoxic activity of some new heterocycles incorporating cyclohepta[b]thiophene‐3‐carboxamide derivatives. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Moustafa A. Gouda
- Department of Chemistry, Faculty of Science and Arts, Ulla Taibah University Medina Saudi Arabia
- Department of Chemistry, Faculty of Science Mansoura University Mansoura Egypt
| | - Mohammed Al‐Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla Taibah University Medina Saudi Arabia
- Department of Chemistry, College of Education Thamar University Dhamar Yemen
| | - Nabil Al‐Zaqri
- Department of Chemistry, College of Science King Saud University Riyadh Saudi Arabia
- Department of Chemistry, College of Science Ibb University Ibb Yemen
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9
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Zhu L, Shan L, Zhu J, Li L, Li S, Wang L, Wang J, Zhang S, Zhou H, Zhang W, Li H. Discovery of a natural fluorescent probe targeting the Plasmodium falciparum cysteine protease falcipain-2. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1016-1025. [PMID: 32048162 DOI: 10.1007/s11427-019-1581-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/26/2019] [Indexed: 01/19/2023]
Abstract
The Plasmodium falciparum cysteine protease falcipain-2 (FP-2) is an attractive antimalarial target. Here, we discovered that the natural compound NP1024 is a nonpeptidic inhibitor of FP-2 with an IC50 value of 0.44 μmol L-1. The most exciting finding is that both in vitro and in vivo, NP1024 directly targets FP-2 in malaria parasite-infected erythrocytes as a natural fluorescent probe, thereby paving the way for an integration of malaria diagnosis and treatment.
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Affiliation(s)
- Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lei Shan
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Junsheng Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Li Li
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Liyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiawei Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Shoude Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Hongchang Zhou
- School of Medicine, Huzhou University, Huzhou Central Hospital, Huzhou, 313000, China
| | - Weidong Zhang
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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10
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Identification of antimalarial leads with dual falcipain-2 and falcipain-3 inhibitory activity. Bioorg Med Chem 2020; 28:115155. [DOI: 10.1016/j.bmc.2019.115155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/26/2019] [Accepted: 10/03/2019] [Indexed: 12/17/2022]
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11
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Design, synthesis and evaluation of 2-(4-(substituted benzoyl)-1,4-diazepan-1-yl)-N-phenylacetamide derivatives as a new class of falcipain-2 inhibitors. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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12
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Aguiar AC, de Sousa LR, Garcia CR, Oliva G, Guido RV. New Molecular Targets and Strategies for Antimalarial Discovery. Curr Med Chem 2019; 26:4380-4402. [DOI: 10.2174/0929867324666170830103003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023]
Abstract
Malaria remains a major health problem, especially because of the emergence
of resistant P. falciparum strains to artemisinin derivatives. In this context, safe and affordable
antimalarial drugs are desperately needed. New proteins have been investigated
as molecular targets for research and development of innovative compounds with welldefined
mechanism of action. In this review, we highlight genetically and clinically validated
plasmodial proteins as drug targets for the next generation of therapeutics. The enzymes
described herein are involved in hemoglobin hydrolysis, the invasion process,
elongation factors for protein synthesis, pyrimidine biosynthesis, post-translational modifications
such as prenylation, phosphorylation and histone acetylation, generation of ATP
in mitochondrial metabolism and aminoacylation of RNAs. Significant advances on proteomics,
genetics, structural biology, computational and biophysical methods provided
invaluable molecular and structural information about these drug targets. Based on this,
several strategies and models have been applied to identify and improve lead compounds.
This review presents the recent progresses in the discovery of antimalarial drug candidates,
highlighting the approaches, challenges, and perspectives to deliver affordable, safe
and low single-dose medicines to treat malaria.
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Affiliation(s)
- Anna Caroline Aguiar
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Lorena R.F. de Sousa
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Celia R.S. Garcia
- Physiology Department, Bioscience Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Rafael V.C. Guido
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
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13
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Wu J, Sun Y, Zhou H, Ma Y, Wang R. Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes. J Biomol Struct Dyn 2019; 38:3156-3165. [PMID: 31402760 DOI: 10.1080/07391102.2019.1654410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 inhibitory activities (IC50) were determined. Among the desired compounds, 1h shares the highest inhibitory activity (IC50 = 1.34 μM) against PTP-MEG2. Additionally, various post-dynamic analyses confirmed that when compound 1h bound to the PTP-MEG2, the protein conformations became unstable and the function of the pTyr recognition loop (Asn331-Cys338) would be disturbed. And thus, the ideal conformations needed for the catalytic activity was difficult to be maintained. In brief, these might be how the compound 1h worked. Furthermore, we also found that the key residues Arg332 would play a critical role in disturbing the residue interactions. AbbreviationsDCCMdynamic cross-correlation mappingDMFN,N-dimethylformamideDSSPdefinition of secondary structure of proteinsFOXOforkhead transcription factorsMDmolecular dynamicsPCAprincipal component analysisPDBprotein data bankPTKsprotein tyrosine kinasesPTPsprotein tyrosine phosphatasesPTP-MEG2megakaryocyte protein tyrosine phosphatase 2RINresidue interaction networkRINGResidue Interaction Network GeneratorRMSDroot means square deviationRMSFroot mean square fluctuationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yingzhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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14
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Alberca LN, Chuguransky SR, Álvarez CL, Talevi A, Salas-Sarduy E. In silico Guided Drug Repurposing: Discovery of New Competitive and Non-competitive Inhibitors of Falcipain-2. Front Chem 2019; 7:534. [PMID: 31448257 PMCID: PMC6691349 DOI: 10.3389/fchem.2019.00534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is among the leading causes of death worldwide. The emergence of Plasmodium falciparum resistant strains with reduced sensitivity to the first line combination therapy and suboptimal responses to insecticides used for Anopheles vector management have led to renewed interest in novel therapeutic options. Here, we report the development and validation of an ensemble of ligand-based computational models capable of identifying falcipain-2 inhibitors, and their subsequent application in the virtual screening of DrugBank and Sweetlead libraries. Among four hits submitted to enzymatic assays, two (odanacatib, an abandoned investigational treatment for osteoporosis and bone metastasis, and the antibiotic methacycline) confirmed inhibitory effects on falcipain-2, with Ki of 98.2 nM and 84.4 μM. Interestingly, Methacycline proved to be a non-competitive inhibitor (α = 1.42) of falcipain-2. The effects of both hits on falcipain-2 hemoglobinase activity and on the development of P. falciparum were also studied.
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Affiliation(s)
- Lucas N Alberca
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sara R Chuguransky
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Cora L Álvarez
- Departamento de Biodiversidad y Biología Experimental, Facultad de Farmacia y Bioquímica, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisico-Química Biológicas (IQUIFIB) "Prof. Alejandro C. Paladini", Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alan Talevi
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde", Universidad Nacional de San Martín, CONICET, Buenos Aires, Argentina
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15
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Stoye A, Juillard A, Tang AH, Legac J, Gut J, White KL, Charman SA, Rosenthal PJ, Grau GER, Hunt NH, Payne RJ. Falcipain Inhibitors Based on the Natural Product Gallinamide A Are Potent in Vitro and in Vivo Antimalarials. J Med Chem 2019; 62:5562-5578. [PMID: 31062592 DOI: 10.1021/acs.jmedchem.9b00504] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A library of analogues of the cyanobacterium-derived depsipeptide natural product gallinamide A were designed and prepared using a highly efficient and convergent synthetic route. Analogues were shown to exhibit potent inhibitory activity against the Plasmodium falciparum cysteine proteases falcipain 2 and falcipain 3 and against cultured chloroquine-sensitive (3D7) and chloroquine-resistant (W2) strains of P. falciparum. Three lead compounds were selected for evaluation of in vivo efficacy against Plasmodium berghei infection in mice on the basis of their improved blood, plasma, and microsomal stability profiles compared with the parent natural product. One of the lead analogues cured P. berghei-infected mice in the Peters 4 day-suppressive test when administered 25 mg kg-1 intraperitoneally daily for 4 days. The compound was also capable of clearing parasites in established infections at 50 mg kg-1 intraperitoneally daily for 4 days and exhibited moderate activity when administered as four oral doses of 100 mg kg-1.
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Affiliation(s)
- Alexander Stoye
- School of Chemistry , Building F11, The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Annette Juillard
- School of Medical Sciences, Sydney Medical School , Building K25, The University of Sydney , Medical Foundation, Sydney , New South Wales 2006 , Australia
| | - Arthur H Tang
- School of Chemistry , Building F11, The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Jennifer Legac
- Department of Medicine, San Francisco General Hospital , University of California , San Francisco , California 94143 , United States
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital , University of California , San Francisco , California 94143 , United States
| | - Karen L White
- Centre for Drug Candidate Optimisation , Monash University , Victoria 3052 , Australia
| | - Susan A Charman
- Centre for Drug Candidate Optimisation , Monash University , Victoria 3052 , Australia
| | - Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital , University of California , San Francisco , California 94143 , United States
| | - Georges E R Grau
- School of Medical Sciences, Sydney Medical School , Building K25, The University of Sydney , Medical Foundation, Sydney , New South Wales 2006 , Australia
| | - Nicholas H Hunt
- School of Medical Sciences, Sydney Medical School , Building K25, The University of Sydney , Medical Foundation, Sydney , New South Wales 2006 , Australia
| | - Richard J Payne
- School of Chemistry , Building F11, The University of Sydney , Sydney , New South Wales 2006 , Australia
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16
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Mishra M, Singh V, Singh S. Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets. Front Microbiol 2019; 10:394. [PMID: 30891019 PMCID: PMC6411711 DOI: 10.3389/fmicb.2019.00394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/14/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria, caused by protozoan of genus Plasmodium, remains one of the highest mortality infectious diseases. Malaria parasites have a complex life cycle, easily adapt to their host’s immune system and have evolved with an arsenal of unique proteases which play crucial roles in proliferation and survival within the host cells. Owing to the existing knowledge of enzymatic mechanisms, 3D structures and active sites of proteases, they have been proven to be opportune for target based drug development. Here, we discuss in depth the crucial roles of essential proteases in Plasmodium life cycle and particularly focus on highlighting the atypical “structural signatures” of key parasite proteases which have been exploited for drug development. These features, on one hand aid parasites pathogenicity while on the other hand could be effective in designing targeted and very specific inhibitors for counteracting them. We conclude that Plasmodium proteases are suitable as multistage targets for designing novel drugs with new modes of action to combat malaria.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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17
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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18
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Oderinlo OO, Tukulula M, Isaacs M, Hoppe HC, Taylor D, Smith VJ, Khanye SD. New thiazolidine-2,4-dione derivatives combined with organometallic ferrocene: Synthesis, structure and antiparasitic activity. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | | | - Michelle Isaacs
- Centre for Chemico- and Biomedicinal Research; Rhodes University; Grahamstown 6140 South Africa
| | - Heinrich C. Hoppe
- Centre for Chemico- and Biomedicinal Research; Rhodes University; Grahamstown 6140 South Africa
- Department of Biochemistry and Microbiology; Rhodes University; Grahamstown 6140 South Africa
| | - Dale Taylor
- Division of Clinical Pharmacology, Department of Medicine; University of Cape Town; Observatory Cape Town 7925 South Africa
| | - Vincent J. Smith
- Department of Chemistry; Rhodes University; Grahamstown 6140 South Africa
- Centre for Chemico- and Biomedicinal Research; Rhodes University; Grahamstown 6140 South Africa
| | - Setshaba D. Khanye
- Department of Chemistry; Rhodes University; Grahamstown 6140 South Africa
- Centre for Chemico- and Biomedicinal Research; Rhodes University; Grahamstown 6140 South Africa
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19
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Identification of Tight-Binding Plasmepsin II and Falcipain 2 Inhibitors in Aqueous Extracts of Marine Invertebrates by the Combination of Enzymatic and Interaction-Based Assays. Mar Drugs 2017; 15:md15040123. [PMID: 28430158 PMCID: PMC5408269 DOI: 10.3390/md15040123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/16/2017] [Accepted: 04/18/2017] [Indexed: 11/18/2022] Open
Abstract
Natural products from marine origin constitute a very promising and underexplored source of interesting compounds for modern biotechnological and pharmaceutical industries. However, their evaluation is quite challenging and requires specifically designed assays to reliably identify the compounds of interest in a highly heterogeneous and interfering context. In the present study, we describe a general strategy for the confident identification of tight-binding protease inhibitors in the aqueous extracts of 62 Cuban marine invertebrates, using Plasmodium falciparum hemoglobinases Plasmepsin II and Falcipain 2 as model enzymes. To this end, we first developed a screening strategy that combined enzymatic with interaction-based assays and then validated screening conditions using five reference extracts. Interferences were evaluated and minimized. The results from the massive screening of such extracts, the validation of several hits by a variety of interaction-based assays and the purification and functional characterization of PhPI, a multifunctional and reversible tight-binding inhibitor for Plasmepsin II and Falcipain 2 from the gorgonian Plexaura homomalla, are presented.
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20
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Li H, Leung KS, Wong MH, Ballester PJ. USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques. Nucleic Acids Res 2016; 44:W436-41. [PMID: 27106057 PMCID: PMC4987897 DOI: 10.1093/nar/gkw320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/06/2016] [Indexed: 12/12/2022] Open
Abstract
Ligand-based Virtual Screening (VS) methods aim at identifying molecules with a similar activity profile across phenotypic and macromolecular targets to that of a query molecule used as search template. VS using 3D similarity methods have the advantage of biasing this search toward active molecules with innovative chemical scaffolds, which are highly sought after in drug design to provide novel leads with improved properties over the query molecule (e.g. patentable, of lower toxicity or increased potency). Ultrafast Shape Recognition (USR) has demonstrated excellent performance in the discovery of molecules with previously-unknown phenotypic or target activity, with retrospective studies suggesting that its pharmacophoric extension (USRCAT) should obtain even better hit rates once it is used prospectively. Here we present USR-VS (http://usr.marseille.inserm.fr/), the first web server using these two validated ligand-based 3D methods for large-scale prospective VS. In about 2 s, 93.9 million 3D conformers, expanded from 23.1 million purchasable molecules, are screened and the 100 most similar molecules among them in terms of 3D shape and pharmacophoric properties are shown. USR-VS functionality also provides interactive visualization of the similarity of the query molecule against the hit molecules as well as vendor information to purchase selected hits in order to be experimentally tested.
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Affiliation(s)
- Hongjian Li
- Institute of Future Cities, Chinese University of Hong Kong, Hong Kong
| | - Kwong-S Leung
- Department of Computer Science and Engineering, Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Man-H Wong
- Department of Computer Science and Engineering, Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, 13009-Marseille, France
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21
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Helal MH, Salem MA, Gouda MA, Ahmed NS, El-Sherif AA. Design, synthesis, characterization, quantum-chemical calculations and anti-inflammatory activity of novel series of thiophene derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 147:73-83. [PMID: 25827768 DOI: 10.1016/j.saa.2015.03.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/22/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
Interaction of 1-(4-morpholinophenyl)ethanone 1 with either malononitrile or ethyl cyanoacetate 2 afforded Knoevenagel-Cope product 3. In subsequent treatment of 3 with sulfur, the 2-aminothiophene derivatives (4a, 4b) are formed under basic conditions. The solvent-free reaction of thiophene derivative 4a with ethyl cyanoacetate afforded thieno[2,3-d][1,3]oxazine derivative 6. The base catalyzed condensation of 2-aminothiophene derivative (4a) with ethyl cyanoacetate afforded N-(thieno-2-yl) cyanoacetamide derivative 7. The latter was used to synthesize different heterocyclic derivatives comprising, pyridine and coumarin rings. Also, several substituted thieno[2,3-d]pyrimidines have been prepared from reaction of 2-aminothiophene-3-carbonitrile 4b with some electrophilic reagents. The structure of the newly compounds were confirmed on the basis of elemental analysis and spectral data. The molecular modeling of the synthesized compounds has been drawn and their molecular parameters were calculated. Also, valuable information is obtained from calculation of the molecular parameters including electronegativity, net dipole moment of the compounds, total energy, electronic energy, binding energy, HOMO and LUMO energy. Evaluation of anti-inflammatory activity of the tested compounds was performed in albino rats by producing carrageenan induced paw oedema and measuring the zone of inflammation at different time intervals i.e. 1, 2, 3 and 4h after carrageenan injection. Results indicated that most of the tested compounds showed moderate to good activity comparable to indomethacin. Also, compound 16 with additional morpholine ring beside the thiophene ring inhibits carrageenan induced paw oedema more than the standard indomethacin drug at all the time scales studied. Thus, compound 16 is considered as a promising compound for further modification to obtain clinically useful anti-inflammatory agent.
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Affiliation(s)
- M H Helal
- Department of Chemistry, Faculty of Arts and Science, Northern Border University, Rafha, Saudi Arabia; Department of Chemistry, Faculty of Science, Al-Azhar University, 11284 Nasr City, Cairo, Egypt
| | - M A Salem
- Department of Chemistry, Faculty of Science, Al-Azhar University, 11284 Nasr City, Cairo, Egypt
| | - M A Gouda
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt; Department of Chemistry, Faculty of Science and Arts, Taibah University, Ulla 41411, Saudi Arabia
| | - N S Ahmed
- Department of Chemistry, Faculty of Arts and Science, Northern Border University, Rafha, Saudi Arabia; Department of Chemistry, National Institute of Oceanography and Fisheres, Alex, Egypt
| | - A A El-Sherif
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt.
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22
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Shave S, Blackburn EA, Adie J, Houston DR, Auer M, Webster SP, Taylor P, Walkinshaw MD. UFSRAT: Ultra-fast Shape Recognition with Atom Types--the discovery of novel bioactive small molecular scaffolds for FKBP12 and 11βHSD1. PLoS One 2015; 10:e0116570. [PMID: 25659145 PMCID: PMC4319890 DOI: 10.1371/journal.pone.0116570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/15/2014] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Using molecular similarity to discover bioactive small molecules with novel chemical scaffolds can be computationally demanding. We describe Ultra-fast Shape Recognition with Atom Types (UFSRAT), an efficient algorithm that considers both the 3D distribution (shape) and electrostatics of atoms to score and retrieve molecules capable of making similar interactions to those of the supplied query. RESULTS Computational optimization and pre-calculation of molecular descriptors enables a query molecule to be run against a database containing 3.8 million molecules and results returned in under 10 seconds on modest hardware. UFSRAT has been used in pipelines to identify bioactive molecules for two clinically relevant drug targets; FK506-Binding Protein 12 and 11β-hydroxysteroid dehydrogenase type 1. In the case of FK506-Binding Protein 12, UFSRAT was used as the first step in a structure-based virtual screening pipeline, yielding many actives, of which the most active shows a KD, app of 281 µM and contains a substructure present in the query compound. Success was also achieved running solely the UFSRAT technique to identify new actives for 11β-hydroxysteroid dehydrogenase type 1, for which the most active displays an IC50 of 67 nM in a cell based assay and contains a substructure radically different to the query. This demonstrates the valuable ability of the UFSRAT algorithm to perform scaffold hops. AVAILABILITY AND IMPLEMENTATION A web-based implementation of the algorithm is freely available at http://opus.bch.ed.ac.uk/ufsrat/.
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Affiliation(s)
- Steven Shave
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth A. Blackburn
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jillian Adie
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas R. Houston
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Scott P. Webster
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Taylor
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
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23
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Hoeger B, Diether M, Ballester PJ, Köhn M. Biochemical evaluation of virtual screening methods reveals a cell-active inhibitor of the cancer-promoting phosphatases of regenerating liver. Eur J Med Chem 2014; 88:89-100. [PMID: 25159123 PMCID: PMC4255093 DOI: 10.1016/j.ejmech.2014.08.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/17/2014] [Accepted: 08/20/2014] [Indexed: 11/30/2022]
Abstract
Computationally supported development of small molecule inhibitors has successfully been applied to protein tyrosine phosphatases in the past, revealing a number of cell-active compounds. Similar approaches have also been used to screen for small molecule inhibitors for the cancer-related phosphatases of regenerating liver (PRL) family. Still, selective and cell-active compounds are of limited availability. Since especially PRL-3 remains an attractive drug target due to its clear role in cancer metastasis, such compounds are highly demanded. In this study, we investigated various virtual screening approaches for their applicability to identify novel small molecule entities for PRL-3 as target. Biochemical evaluation of purchasable compounds revealed ligand-based approaches as well suited for this target, compared to docking-based techniques that did not perform well in this context. The best hit of this study, a 2-cyano-2-ene-ester and hence a novel chemotype targeting the PRLs, was further optimized by a structure–activity-relationship (SAR) study, leading to a low micromolar PRL inhibitor with acceptable selectivity over other protein tyrosine phosphatases. The compound is active in cells, as shown by its ability to specifically revert PRL-3 induced cell migration, and exhibits similar effects on PRL-1 and PRL-2. It is furthermore suitable for fluorescence microscopy applications, and it is commercially available. These features make it the only purchasable, cell-active and acceptably selective PRL inhibitor to date that can be used in various cellular applications. Computational ligand- and docking-based approaches were tested for PRL-3 as a target. Ligand-based screening was proven a feasible approach for PRL-3 inhibitor discovery. A low micromolar, non-competitive inhibitor with novel chemotype for PRLs was discovered. The inhibitor efficiently blocks PRL induced cell migration. The inhibitor is non-cytotoxic, commercially available and suitable for fluorescence microscopy applications.
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Affiliation(s)
- Birgit Hoeger
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Maren Diether
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Pedro J Ballester
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom; Inserm U1068, Centre de Recherche en Cancérologie de Marseille, France.
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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24
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Identification of diverse natural products as falcipain-2 inhibitors through structure-based virtual screening. Bioorg Med Chem Lett 2014; 24:1261-4. [DOI: 10.1016/j.bmcl.2014.01.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/01/2014] [Accepted: 01/23/2014] [Indexed: 11/21/2022]
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25
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Chen B, Ni H, Guo X, Zhang G, Yu Y. Facile preparation of 3,5-disubstituted-4-aminothiophene-2-carbaldehyde from a novel unexpected domino reaction of vinyl azides and 1,4-dithiane-2,5-diol. RSC Adv 2014. [DOI: 10.1039/c4ra08649j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A facile approach to provide 3,5-disubstituted-4-aminothiophene-2-carbaldehyde containing both the amino group and the aldehyde group has been developed.
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Affiliation(s)
- Binhui Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Science
- Zhejiang University
- Hangzhou 310058, P. R. China
| | - Hangcheng Ni
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Science
- Zhejiang University
- Hangzhou 310058, P. R. China
| | - Xiao Guo
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Science
- Zhejiang University
- Hangzhou 310058, P. R. China
| | - Guolin Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Science
- Zhejiang University
- Hangzhou 310058, P. R. China
| | - Yongping Yu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Science
- Zhejiang University
- Hangzhou 310058, P. R. China
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26
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Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC. Novel anti-plasmodial hits identified by virtual screening of the ZINC database. J Comput Aided Mol Des 2013; 27:859-71. [PMID: 24158745 DOI: 10.1007/s10822-013-9685-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/12/2013] [Indexed: 01/16/2023]
Abstract
Increased resistance of Plasmodium falciparum to most available drugs challenges the control of malaria. Studies with protease inhibitors have suggested important roles for the falcipain family of cysteine proteases. These enzymes act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. In order to find potential new antimalarial drugs, we screened in silico the ZINC database using two different protocols involving structure- and ligand-based methodologies. Our search identified 19 novel low micromolar inhibitors of cultured chloroquine resistant P. falciparum. The most active compound presented an IC50 value of 0.5 μM against cultured parasites and it also inhibited the cysteine protease falcipain-2 (IC50 = 25.5 μM). These results identify novel classes of antimalarials that are structurally different from those currently in use and which can be further derivatized to deliver leads suitable for optimisation.
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Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
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27
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Xu M, Zhu J, Diao Y, Zhou H, Ren X, Sun D, Huang J, Han D, Zhao Z, Zhu L, Xu Y, Li H. Novel Selective and Potent Inhibitors of Malaria Parasite Dihydroorotate Dehydrogenase: Discovery and Optimization of Dihydrothiophenone Derivatives. J Med Chem 2013; 56:7911-24. [DOI: 10.1021/jm400938g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Hongchang Zhou
- Department
of Microbiology, Medical School of Huzhou Teachers College, Huzhou 313000, China
| | | | | | | | - Dongmei Han
- Instrumental
Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
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28
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Marques AF, Esser D, Rosenthal PJ, Kassack MU, Lima LMTR. Falcipain-2 inhibition by suramin and suramin analogues. Bioorg Med Chem 2013; 21:3667-73. [PMID: 23680445 DOI: 10.1016/j.bmc.2013.04.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/09/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
Abstract
Falcipain-2 is a cysteine protease of the malaria parasite Plasmodium falciparum that plays a key role in the hydrolysis of hemoglobin, a process that is required by intraerythrocytic parasites to obtain amino acids. In this work we show that the polysulfonated napthylurea suramin is capable of binding to falcipain-2, inhibiting its catalytic activity at nanomolar concentrations against both synthetic substrates and the natural substrate hemoglobin. Kinetic measurements suggest that the inhibition occurs through an noncompetitive allosteric mechanism, eliciting substrate inhibition. Smaller suramin analogues and those with substituted methyl groups also showed inhibition within the nanomolar range. Our results identify the suramin family as a potential starting point for the design of falcipain-2 inhibitor antimalarials that act through a novel inhibition mechanism.
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Affiliation(s)
- Adriana Fonseca Marques
- Laboratory for Pharmaceutical Biotechnology, School of Pharmacy, Federal University of Rio de Janeiro, CCS, Bss34, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
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29
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Madhavi Sastry G, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 2013; 27:221-34. [DOI: 10.1007/s10822-013-9644-8] [Citation(s) in RCA: 2913] [Impact Index Per Article: 264.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 04/03/2013] [Indexed: 12/11/2022]
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30
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Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments. J Mol Graph Model 2013; 41:20-30. [DOI: 10.1016/j.jmgm.2013.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 01/15/2023]
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31
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Venkata Rao K, Balakumar C, Lakshmi Narayana B, Pran Kishore D, Rajwinder K, Raghuram Rao A. Transesterification of trimethyl orthoacetate: an efficient protocol for the synthesis of 4-alkoxy-2-aminothiophene-3-carbonitriles. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2012.12.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Mane UR, Gupta RC, Nadkarni SS, Giridhar RR, Naik PP, Yadav MR. Falcipain inhibitors as potential therapeutics for resistant strains of malaria: a patent review. Expert Opin Ther Pat 2012; 23:165-87. [DOI: 10.1517/13543776.2013.743992] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Schreyer AM, Blundell T. USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints. J Cheminform 2012; 4:27. [PMID: 23131020 PMCID: PMC3505738 DOI: 10.1186/1758-2946-4-27] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 11/01/2012] [Indexed: 12/31/2022] Open
Abstract
Background Ligand-based virtual screening using molecular shape is an important tool for researchers who wish to find novel chemical scaffolds in compound libraries. The Ultrafast Shape Recognition (USR) algorithm is capable of screening millions of compounds and is therefore suitable for usage in a web service. The algorithm however is agnostic of atom types and cannot discriminate compounds with similar shape but distinct pharmacophoric features. To solve this problem, an extension of USR called USRCAT, has been developed that includes pharmacophoric information whilst retaining the performance benefits of the original method. Results The USRCAT extension is shown to outperform the traditional USR method in a retrospective virtual screening benchmark. Also, a relational database implementation is described that is capable of screening a million conformers in milliseconds and allows the inclusion of complex query parameters. Conclusions USRCAT provides a solution to the lack of atom type information in the USR algorithm. Researchers, particularly those with only limited resources, who wish to use ligand-based virtual screening in order to discover new hits, will benefit the most. Online chemical databases that offer a shape-based similarity method might also find advantage in using USRCAT due to its accuracy and performance. The source code is freely available and can easily be modified to fit specific needs.
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Affiliation(s)
- Adrian M Schreyer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, United Kingdom.
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34
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Synthesis and biological activities of novel artemisinin derivatives as cysteine protease falcipain-2 inhibitors. Arch Pharm Res 2012; 35:1525-31. [DOI: 10.1007/s12272-012-0902-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 06/26/2011] [Accepted: 07/21/2011] [Indexed: 10/27/2022]
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35
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Diao Y, Lu W, Jin H, Zhu J, Han L, Xu M, Gao R, Shen X, Zhao Z, Liu X, Xu Y, Huang J, Li H. Discovery of diverse human dihydroorotate dehydrogenase inhibitors as immunosuppressive agents by structure-based virtual screening. J Med Chem 2012; 55:8341-9. [PMID: 22984987 DOI: 10.1021/jm300630p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study applied an efficient virtual screening strategy integrating molecular docking with MM-GBSA rescoring to identify diverse human dihydroorotate dehydrogenase (hDHODH) inhibitors. Eighteen compounds with IC(50) values ranging from 0.11 to 18.8 μM were identified as novel hDHODH inhibitors that exhibited overall species-selectivity over Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH). Compound 8, the most potent one, showed low micromolar inhibitory activity against hDHODH with an IC(50) value of 0.11 μM. Moreover, lipopolysaccharide-induced B-cell assay and mixed lymphocyte reaction assay revealed that most of the hits showed potent antiproliferative activity against B and T cells, which demonstrates their potential application as immunosuppressive agents. In particular, compound 18 exhibited potent B-cell inhibitory activity (IC(50) = 1.78 μM) and presents a B-cell-specific profile with 17- and 26-fold selectivities toward T and Jurkat cells, respectively.
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Affiliation(s)
- Yanyan Diao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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36
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Ballester PJ, Mangold M, Howard NI, Robinson RLM, Abell C, Blumberger J, Mitchell JBO. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification. J R Soc Interface 2012; 9:3196-207. [PMID: 22933186 PMCID: PMC3481598 DOI: 10.1098/rsif.2012.0569] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.
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Affiliation(s)
- Pedro J Ballester
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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37
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One-pot synthesis of thieno [2,3-d] pyrimidin-4-ol derivatives mediated by polyphosphonic anhydride. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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38
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Shah F, Gut J, Legac J, Shivakumar D, Sherman W, Rosenthal PJ, Avery MA. Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis. J Chem Inf Model 2012; 52:696-710. [PMID: 22332946 DOI: 10.1021/ci2005516] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure-activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand-protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand-protein interactions.
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Affiliation(s)
- Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, USA
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39
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Design and synthesis of small molecular dual inhibitor of falcipain-2 and dihydrofolate reductase as antimalarial agent. Bioorg Med Chem Lett 2012; 22:958-62. [DOI: 10.1016/j.bmcl.2011.12.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 11/09/2011] [Accepted: 12/03/2011] [Indexed: 11/20/2022]
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40
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Zheng ZJ, Liu LX, Gao G, Dong H, Jiang JX, Lai GQ, Xu LW. Amine-functional polysiloxanes (AFPs) as efficient polymeric organocatalyst for amino catalysis: efficient multicomponent Gewald reaction, α-allylic alkylation of aldehydes, and Knoevenagel condensation. RSC Adv 2012. [DOI: 10.1039/c2ra00029f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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Luo W, Lu WQ, Cui KQ, Liu Y, Wang J, Guo C. N 1-{4-[(10S)-Dihydroartemisinin-10-oxyl]}phenylmethylene-N 2-(2-methylquinoline-4-yl)hydrazine derivatives as antiplasmodial falcipain-2 inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9854-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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42
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Hansen G, Heitmann A, Witt T, Li H, Jiang H, Shen X, Heussler VT, Rennenberg A, Hilgenfeld R. Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium. Structure 2011; 19:919-29. [PMID: 21742259 DOI: 10.1016/j.str.2011.03.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 11/17/2022]
Abstract
Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 Å X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.
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Affiliation(s)
- Guido Hansen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lübeck, Germany
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43
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Discovery of novel human acrosin inhibitors by virtual screening. J Comput Aided Mol Des 2011; 25:977-85. [DOI: 10.1007/s10822-011-9476-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 01/04/2011] [Indexed: 10/17/2022]
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44
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Rodrigues T, Moreira R, Gut J, Rosenthal PJ, O Neill PM, Biagini GA, Lopes F, dos Santos DJVA, Guedes RC. Identification of new antimalarial leads by use of virtual screening against cytochrome bc₁. Bioorg Med Chem 2011; 19:6302-8. [PMID: 21958736 DOI: 10.1016/j.bmc.2011.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Cytochrome bc(1) is a validated drug target in malaria parasites. The spread of Plasmodium falciparum strains resistant to multiple antimalarials emphasizes the urgent need for new drugs. We screened in silico the ZINC and MOE databases, using ligand- and structure-based approaches, to identify new leads for development. The most active compound presented an IC(50) value against cultured P. falciparum of 2 μM and a docking pose consistent with its activity.
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Affiliation(s)
- Tiago Rodrigues
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-019 Lisbon, Portugal
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45
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Huang XG, Liu J, Ren J, Wang T, Chen W, Zeng BB. A facile and practical one-pot synthesis of multisubstituted 2-aminothiophenes via imidazole-catalyzed Gewald reaction. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.061] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Abstract
Molecular shape complementarity is widely recognized as a key indicator of biological activity. Unfortunately, efficient computation of shape similarity is challenging, which severely limits the potential of shape-based virtual screening. Ultrafast shape recognition (USR) is a recent shape similarity technique that is characterized by its extremely high speed of operation. Here we review important methodological aspects for the optimal application of USR as well as its first applications to medicinal chemistry problems. These applications already include several particularly successful prospective virtual screens, which shows the important role that USR can play in identifying bioactive molecules to be used as chemical probes and potentially as starting points for the drug-discovery process.
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47
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Matter H, Sotriffer C. Applications and Success Stories in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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48
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Shah F, Mukherjee P, Gut J, Legac J, Rosenthal PJ, Tekwani BL, Avery MA. Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library. J Chem Inf Model 2011; 51:852-64. [PMID: 21428453 DOI: 10.1021/ci200029y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.
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Affiliation(s)
- Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi , University, Mississippi 38677, USA
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49
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Rosenthal PJ. Falcipains and other cysteine proteases of malaria parasites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 712:30-48. [PMID: 21660657 DOI: 10.1007/978-1-4419-8414-2_3] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of cysteine proteases of malaria parasites have been described and many more are suggested by analysis of the Plasmodium falciparum genome sequence. The best characterized of these proteases are the falcipains, a family of four papain-family enzymes. Falcipain-2 and falcipain-3 act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. Disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis and parasites with increased sensitivity to protease inhibitors. Disruption of the falcipain-3 gene was not possible, strongly suggesting that this protease is essential for erythrocytic parasites. Disruption of the falcipain-1 gene did not alter development in erythrocytes, but led to decreased production of oocysts in mosquitoes. other papain-family proteases predicted by the genome sequence include dipeptidyl peptidases, a calpain homolog and serine-repeat antigens (SERAs). Dipeptidyl aminopeptidase 1 appears to be essential and localized to the food vacuole, suggesting a role in hemoglobin hydrolysis. Dipeptidyl aminopeptidase 3 appears to play a role in the rupture of erythrocytes by mature parasites. the P. falciparum calpain homolog gene could not be disrupted, suggesting that the protein is essential and a role in the parasite cell cycle has been suggested. Nine P. falciparum SERAs have cysteine protease motifs, but in some the active site cys is replaced by a Ser. Gene disruption studies suggested that SERA-5 and SERA-6 are essential. activation of SERA-5 by a serine protease seems to be required for merozoite egress from the erythrocyte. New drugs for malaria are greatly needed and cysteine proteases represent potential drug targets. cysteine protease inhibitors have demonstrated potent antimalarial effects and the optimization and testing of falcipain inhibitor antimalarials is underway.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA.
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50
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Dong G, Sheng C, Wang S, Miao Z, Yao J, Zhang W. Selection of evodiamine as a novel topoisomerase I inhibitor by structure-based virtual screening and hit optimization of evodiamine derivatives as antitumor agents. J Med Chem 2010; 53:7521-31. [PMID: 20942490 DOI: 10.1021/jm100387d] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human topoisomerase I (TopoI) is recognized as a valuable target for the development of effective antitumor agents. Structure-based virtual screening was applied to the discovery of structurally diverse TopoI inhibitors. From 23 compounds selected by virtual screening, a total of 14 compounds were found to be TopoI inhibitors. Five hits (compounds 1, 14, 20, 21, and 23) also showed moderate to good in vitro antitumor activity. These novel structures can be considered as good starting points for the development of new antitumor lead compounds. Hit 20 (evodiamine) was chosen for preliminary structure-activity relationship studies. Various groups, including alkyl, benzoyl, benzyl and ester, were introduced to the indole nitrogen atom of evodiamine. The substituted benzoyl groups were found to be favorable for the antitumor activity and spectrum. The 4-Cl benzoyl derivative, compound 29u, was the most active one with IC(50) values in the range 0.049-2.6 μM.
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Affiliation(s)
- Guoqiang Dong
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China
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