1
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Chen M, Lan H, Yao S, Jin K, Chen Y. Metabolic Interventions in Tumor Immunity: Focus on Dual Pathway Inhibitors. Cancers (Basel) 2023; 15:cancers15072043. [PMID: 37046703 PMCID: PMC10093048 DOI: 10.3390/cancers15072043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
The metabolism of tumors and immune cells in the tumor microenvironment (TME) can affect the fate of cancer and immune responses. Metabolic reprogramming can occur following the activation of metabolic-related signaling pathways, such as phosphoinositide 3-kinases (PI3Ks) and the mammalian target of rapamycin (mTOR). Moreover, various tumor-derived immunosuppressive metabolites following metabolic reprogramming also affect antitumor immune responses. Evidence shows that intervention in the metabolic pathways of tumors or immune cells can be an attractive and novel treatment option for cancer. For instance, administrating inhibitors of various signaling pathways, such as phosphoinositide 3-kinases (PI3Ks), can improve T cell-mediated antitumor immune responses. However, dual pathway inhibitors can significantly suppress tumor growth more than they inhibit each pathway separately. This review discusses the latest metabolic interventions by dual pathway inhibitors as well as the advantages and disadvantages of this therapeutic approach.
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Affiliation(s)
- Min Chen
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Huanrong Lan
- Department of Surgical Oncology, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China
| | - Shiya Yao
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Ketao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yun Chen
- Department of Colorectal Surgery, Xinchang People's Hospital, Affiliated Xinchang Hospital, Wenzhou Medical University, Xinchang 312500, China
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2
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Naseem S, Shafiq Z, Taslimi P, Hussain S, Taskin-Tok T, Kisa D, Saeed A, Temirak A, Tahir MN, Rauf K, El-Gokha A. Synthesis and evaluation of novel xanthene-based thiazoles as potential antidiabetic agents. Arch Pharm (Weinheim) 2023; 356:e2200356. [PMID: 36220614 DOI: 10.1002/ardp.202200356] [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: 07/10/2022] [Revised: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023]
Abstract
A series of xanthene-based thiazoles was synthesized and characterized by different scpectroscopic methods, i.e. Proton nuclear magnetic resonance (1 H NMR), carbon nuclear magnetic resonance (13 C NMR), infrared spectroscopy, carbon hydrogen nitrogen analysis, and X-ray crystallography. The inhibition potencies of 18 newly synthesized thiazole derivatives were investigated on the activities of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-amylase (α-Amy), and α-glycosidase (α-Gly) enzymes in accordance with their antidiabetic and anticholinesterase ability. The synthesized compounds have the highest inhibition potential against the enzymes at low nanomolar concentrations. Among the 18 newly synthesized molecules, 3b and 3p were superior to the known commercial inhibitors of the enzymes and have a much more effective inhibitory potential, with IC50 : 2.37 and 1.07 nM for AChE, 0.98 and 0.59 nM for BChE, 56.47 and 61.34 nM for α-Gly, and 152.48 and 124.84 nM for α-Amy, respectively. Finally, the optimized 18 compounds were subjected to molecular docking to describe the interaction between thiazole derivatives and AChE, BChE, α-Amy, and α-Gly enzymes in which important interactions were monitored with amino acid residues of each target enzyme.
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Affiliation(s)
- Saira Naseem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan.,Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey.,Department of Chemistry, Faculty of Science, Istinye University, Istanbul, Turkey
| | - Saghir Hussain
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | - Dursun Kisa
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ahmed Temirak
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Muhammad N Tahir
- Department of Physics, University of Sargodha, Sargodha, Pakistan
| | - Khawar Rauf
- Department of Chemistry, Govt. Post-Graduate Gordon College, Rawalpindi, Pakistan
| | - Ahmed El-Gokha
- Chemistry Department, Faculty of Science, Menoufia University, Menoufia, Egypt
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3
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Das BK, Chakraborty D. Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments. J Biomol Struct Dyn 2022; 40:13083-13102. [PMID: 34581241 DOI: 10.1080/07391102.2021.1981452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental KD ∼ 100-.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔGbind-eff = -62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔGbind-eff = -71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors.
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Affiliation(s)
- Bratin Kumar Das
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
| | - Debashree Chakraborty
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
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4
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Shamshad H, Bakri R, Mirza AZ. Dihydrofolate reductase, thymidylate synthase, and serine hydroxy methyltransferase: successful targets against some infectious diseases. Mol Biol Rep 2022; 49:6659-6691. [PMID: 35253073 PMCID: PMC8898753 DOI: 10.1007/s11033-022-07266-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Parasitic diseases have a serious impact on the world in terms of health and economics and are responsible for worldwide mortality and morbidity. The present review features the hybrid targeting involving three main enzymes for the treatment of different parasitic diseases. The enzymes Dihydrofolate reductase, thymidylate synthase, and Serine hydroxy methyltransferase play an essential role in the folate pathway. The present review focuses on these enzymes, which can be targeted against several diseases. It shed light on the past, present, and future of these targets, and it can be assessed that these targets can play a significant role against several infectious diseases. For combating viral and protozoal infectious diseases, these targets in combination should be addressed.
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Affiliation(s)
- Hina Shamshad
- Faculty of Pharmacy, Jinnah University for Women, Karachi, Pakistan
| | - Rowaida Bakri
- College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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5
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The Complementarity Principle-One More Step towards Analytical Docking on the Example of Dihydrofolate Reductase Complexes. Life (Basel) 2021; 11:life11090983. [PMID: 34575132 PMCID: PMC8469765 DOI: 10.3390/life11090983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
New approaches to assessing the “enzyme–ligand” complementarity, taking into account hydrogens, have been proposed. The approaches are based on the calculation of three-dimensional maps of the electron density of the receptor–ligand complexes. The action of complementarity factors, first proposed in this article, has been demonstrated on complexes of human dihydrofolate reductase (DHFR) with ligands. We found that high complementarity is ensured by the formation of the most effective intermolecular contacts, which are provided due to predominantly paired atomic–atomic interactions, while interactions of the bifurcate and more disoriented type are minimized. An analytical docking algorithm based on the proposed receptor–ligand complementarity factors is proposed.
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6
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Thesnaar L, Bezuidenhout JJ, Petzer A, Petzer JP, Cloete TT. Methylene blue analogues: In vitro antimicrobial minimum inhibitory concentrations and in silico pharmacophore modelling. Eur J Pharm Sci 2021; 157:105603. [DOI: 10.1016/j.ejps.2020.105603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 01/05/2023]
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7
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Design, synthesis, biological assessment and molecular docking studies of some new 2-Thioxo-2,3-dihydropyrimidin-4(1H)-ones as potential anticancer and antibacterial agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Naumovich V, Grishina M, Novak J, Pathak P, Potemkin V, Shahbaaz M, Abdellattif MH. Electronic properties investigation of human dihydrofolate reductase complexes with ligands. J Biomol Struct Dyn 2020; 40:4775-4790. [PMID: 33345753 DOI: 10.1080/07391102.2020.1861985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Despite the fact that there are already drugs for cancer, they still show strong toxicity to the human organism. That is why it is necessary to establish the factors affecting activity in order to develop new, more effective drugs aimed at tumor cells, minimizing harm to healthy cells. The present research is based on electronic properties calculation of the complexes using AlteQ approach. In the focus of this study are complexes of human dihydrofolate reductase (hDHFR) with a series of known inhibitors bound in the active site. Further, a statistical analysis was performed to establish the relationships between a myriad electronic characteristics and IC50. The change in total volume and the change of own electrons number of hydrogen atoms in their atomic basins are identified as the descriptors correlating the most with the hDHFR inhibition potency. Additionally, two lipophilic parts of protein (Thr56, Ser59, Ile60 and Ile7, Val8, Ala9) were found, which act as a key factor in decreasing bioactivity. The depth analysis of intermolecular interactions showed that the interactions between water molecules and ligand play a crucial role in hDHFR inhibition. Furthermore, the molecular dynamics simulations were used for deeper understanding of the structural inhibition, each for 50 ns time scale in explicit water conditions. Thus, the AlteQ approach made it possible to determine the factors influencing the activity and evaluate them not only qualitatively, but also quantitatively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mohd Shahbaaz
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia.,South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
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9
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Toulouse JL, Shi G, Lemay-St-Denis C, Ebert MCCJC, Deon D, Gagnon M, Ruediger E, Saint-Jacques K, Forge D, Vanden Eynde JJ, Marinier A, Ji X, Pelletier JN. Dual-Target Inhibitors of the Folate Pathway Inhibit Intrinsically Trimethoprim-Resistant DfrB Dihydrofolate Reductases. ACS Med Chem Lett 2020; 11:2261-2267. [PMID: 33214838 DOI: 10.1021/acsmedchemlett.0c00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
Trimethoprim (TMP) is widely used to treat infections in humans and in livestock, accelerating the incidence of TMP resistance. The emergent and largely untracked type II dihydrofolate reductases (DfrBs) are intrinsically TMP-resistant plasmid-borne Dfrs that are structurally and evolutionarily unrelated to chromosomal Dfrs. We report kinetic characterization of the known DfrB family members. Their kinetic constants are conserved and all are poorly inhibited by TMP, consistent with TMP resistance. We investigate their inhibition with known and novel bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK). Importantly, all are inhibited by the HPPK inhibitors, making these molecules dual-target inhibitors of two folate pathway enzymes that are strictly microbial.
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Affiliation(s)
- Jacynthe L. Toulouse
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | - Genbin Shi
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Claudèle Lemay-St-Denis
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | | | - Daniel Deon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Marc Gagnon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Edward Ruediger
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Kévin Saint-Jacques
- Département de chimie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Delphine Forge
- Laboratoire de chimie organique, Université de Mons, 7000 Mons, Belgium
| | | | - Anne Marinier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Joelle N. Pelletier
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
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10
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Mitra K, Ghanta P, Acharya S, Chakrapani G, Ramaiah B, Doble M. Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads. J Biomol Struct Dyn 2020; 39:6324-6337. [PMID: 32698693 PMCID: PMC7441782 DOI: 10.1080/07391102.2020.1796802] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SARS-related coronaviruses poses continual threat to humanity by rapidly mutating and emerging as severe pandemic outbreaks, including the current nCoV-19 pandemic. Hence a rapid drug repositioning and lead identification strategy are required to mitigate these outbreaks. We report a pharmacophore and molecular dynamics-based approach for drug repositioning and lead identification against dual targets (3CLp and PLp) of SARS-CoV-2. The pharmacophore model of 3CLp inhibitors was apolar with two aromatic and two H-bond acceptors, whereas that of PLp was relatively polar, bearing one aromatic and three H-bond acceptors. Pharmacophore-based virtual screening yielded six existing FDA-approved drugs and twelve natural products with both the pharmacophoric features. Among them are nelfinavir, tipranavir and licochalcone-D, which has shown better binding characteristics with both the proteases compared to lopinavir. The molecular dynamics revealed that the connecting loop (residues 176–199) of 3CLp is highly flexible, and hence, inhibitors should avoid high-affinity interactions with it. Lopinavir, due to its high affinity with the loop region, exhibited unstable binding. Further, the van der Waals size of the 3CLp inhibitors positively correlated with their binding affinity with 3CLp. However, the van der Waals size of a ligand should not cross a threshold of 572Å3, beyond which the ligands are likely to make high-affinity interaction with the loop and suffer unstable binding as observed in the case of lopinavir. Similarly, the total polar surface area of the ligands were found to be negatively correlated with their binding affinity with PLp.
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Affiliation(s)
- Kartik Mitra
- Department of Biotechnology, Bio-Engineering and Drug Design Lab, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Adayar, Chennai, Tamil Nadu, India
| | - Prasanth Ghanta
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Sushank Acharya
- Department of Biotechnology, Bio-Engineering and Drug Design Lab, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Adayar, Chennai, Tamil Nadu, India
| | - Gayathri Chakrapani
- Department of Biotechnology, Bio-Engineering and Drug Design Lab, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Adayar, Chennai, Tamil Nadu, India
| | - Basavaraju Ramaiah
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Mukesh Doble
- Department of Biotechnology, Bio-Engineering and Drug Design Lab, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Adayar, Chennai, Tamil Nadu, India
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11
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Ahmed MH, El‐Hashash MA, Marzouk MI, El‐Naggar AM. Synthesis and antitumor activity of some nitrogen heterocycles bearing pyrimidine moiety. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marwa H. Ahmed
- Chemistry Department, Faculty of ScienceAin Shams University Abbassia, Cairo Egypt
| | - Maher A. El‐Hashash
- Chemistry Department, Faculty of ScienceAin Shams University Abbassia, Cairo Egypt
| | - Magda I. Marzouk
- Chemistry Department, Faculty of ScienceAin Shams University Abbassia, Cairo Egypt
| | - Abeer M. El‐Naggar
- Chemistry Department, Faculty of ScienceAin Shams University Abbassia, Cairo Egypt
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12
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Dual-target kinase drug design: Current strategies and future directions in cancer therapy. Eur J Med Chem 2020; 188:112025. [DOI: 10.1016/j.ejmech.2019.112025] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/18/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022]
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13
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Dual-targeted hit identification using pharmacophore screening. J Comput Aided Mol Des 2019; 33:955-964. [PMID: 31691918 DOI: 10.1007/s10822-019-00245-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/30/2019] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis infection remains a major cause of global morbidity and mortality due to the increase of antibiotics resistance. Dual/multi-target drug discovery is a promising approach to overcome bacterial resistance. In this study, we built ligand-based pharmacophore models and performed pharmacophore screening in order to identify hit compounds targeting simultaneously two enzymes-M. tuberculosis leucyl-tRNA synthetase (LeuRS) and methionyl-tRNA synthetase (MetRS). In vitro aminoacylation assay revealed five compounds from different chemical classes inhibiting both enzymes. Among them the most active compound-3-(3-chloro-4-methoxy-phenyl)-5-[3-(4-fluoro-phenyl)-[1,2,4]oxadiazol-5-yl]-3H-[1,2,3]triazol-4-ylamine (1) inhibits mycobacterial LeuRS and MetRS with IC50 values of 13 µM and 13.8 µM, respectively. Molecular modeling study indicated that compound 1 has similar binding mode with the active sites of both aminoacyl-tRNA synthetases and can be valuable compound for further chemical optimization in order to find promising antituberculosis agents.
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14
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Dihydrofolate reductase inhibition effect of 5-substituted pyrido[2,3-d]pyrimidines: Synthesis, antitumor activity and molecular modeling study. Bioorg Chem 2019; 90:103076. [DOI: 10.1016/j.bioorg.2019.103076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
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15
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DHFR Inhibitors: Reading the Past for Discovering Novel Anticancer Agents. Molecules 2019; 24:molecules24061140. [PMID: 30909399 PMCID: PMC6471984 DOI: 10.3390/molecules24061140] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/17/2022] Open
Abstract
Dihydrofolate reductase inhibitors are an important class of drugs, as evidenced by their use as antibacterial, antimalarial, antifungal, and anticancer agents. Progress in understanding the biochemical basis of mechanisms responsible for enzyme selectivity and antiproliferative effects has renewed the interest in antifolates for cancer chemotherapy and prompted the medicinal chemistry community to develop novel and selective human DHFR inhibitors, thus leading to a new generation of DHFR inhibitors. This work summarizes the mechanism of action, chemical, and anticancer profile of the DHFR inhibitors discovered in the last six years. New strategies in DHFR drug discovery are also provided, in order to thoroughly delineate the current landscape for medicinal chemists interested in furthering this study in the anticancer field.
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16
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Srinivasan B, Tonddast-Navaei S, Roy A, Zhou H, Skolnick J. Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs. Med Res Rev 2018; 39:684-705. [PMID: 30192413 DOI: 10.1002/med.21538] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/16/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
Escherichia coli Dihydrofolate reductase is an important enzyme that is essential for the survival of the Gram-negative microorganism. Inhibitors designed against this enzyme have demonstrated application as antibiotics. However, either because of poor bioavailability of the small-molecules resulting from their inability to cross the double membrane in Gram-negative bacteria or because the microorganism develops resistance to the antibiotics by mutating the DHFR target, discovery of new antibiotics against the enzyme is mandatory to overcome drug-resistance. This review summarizes the field of DHFR inhibition with special focus on recent efforts to effectively interface computational and experimental efforts to discover novel classes of inhibitors that target allosteric and active-sites in drug-resistant variants of EcDHFR.
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Affiliation(s)
- Bharath Srinivasan
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia
| | - Sam Tonddast-Navaei
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia
| | - Ambrish Roy
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia
| | - Hongyi Zhou
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia
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17
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Proschak E, Stark H, Merk D. Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds. J Med Chem 2018; 62:420-444. [PMID: 30035545 DOI: 10.1021/acs.jmedchem.8b00760] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multitargeting compounds comprising activity on more than a single biological target have gained remarkable relevance in drug discovery owing to the complexity of multifactorial diseases such as cancer, inflammation, or the metabolic syndrome. Polypharmacological drug profiles can produce additive or synergistic effects while reducing side effects and significantly contribute to the high therapeutic success of indispensable drugs such as aspirin. While their identification has long been the result of serendipity, medicinal chemistry now tends to design polypharmacology. Modern in vitro pharmacological methods and chemical probes allow a systematic search for rational target combinations and recent innovations in computational technologies, crystallography, or fragment-based design equip multitarget compound development with valuable tools. In this Perspective, we analyze the relevance of multiple ligands in drug discovery and the versatile toolbox to design polypharmacology. We conclude that despite some characteristic challenges remaining unresolved, designed polypharmacology holds enormous potential to secure future therapeutic innovation.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , Universitaetsstrasse 1 , D-40225 , Duesseldorf , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany.,Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences , Swiss Federal Institute of Technology (ETH) Zürich , Vladimir-Prelog-Weg 4 , CH-8093 Zürich , Switzerland
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18
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Synthesis and evaluation of new 2,6-diamino-5-hetarylpyrimidines as inhibitors of dihydrofolate reductase. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-017-2032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Kumar A, Sharma A. Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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20
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Kalash L, Val C, Azuaje J, Loza MI, Svensson F, Zoufir A, Mervin L, Ladds G, Brea J, Glen R, Sotelo E, Bender A. Computer-aided design of multi-target ligands at A 1R, A 2AR and PDE10A, key proteins in neurodegenerative diseases. J Cheminform 2017; 9:67. [PMID: 29290010 PMCID: PMC5748027 DOI: 10.1186/s13321-017-0249-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/01/2017] [Indexed: 01/30/2023] Open
Abstract
Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may be useful in treating neurodegenerative diseases by promoting neuronal survival in a synergistic manner via their multi-target activity at the adenosine A1 and A2A receptors (A1R and A2AR) and phosphodiesterase 10A (PDE10A), which modulate intracellular cAMP levels. Hence, in this work we describe a computational method for the design of synthetically feasible ligands that bind to A1 and A2A receptors and inhibit phosphodiesterase 10A (PDE10A), involving a retrosynthetic approach employing in silico target prediction and docking, which may be generally applicable to multi-target compound design at several target classes. This approach has identified 2-aminopyridine-3-carbonitriles as the first multi-target ligands at A1R, A2AR and PDE10A, by showing agreement between the ligand and structure based predictions at these targets. The series were synthesized via an efficient one-pot scheme and validated pharmacologically as A1R/A2AR-PDE10A ligands, with IC50 values of 2.4-10.0 μM at PDE10A and Ki values of 34-294 nM at A1R and/or A2AR. Furthermore, selectivity profiling of the synthesized 2-amino-pyridin-3-carbonitriles against other subtypes of both protein families showed that the multi-target ligand 8 exhibited a minimum of twofold selectivity over all tested off-targets. In addition, both compounds 8 and 16 exhibited the desired multi-target profile, which could be considered for further functional efficacy assessment, analog modification for the improvement of selectivity towards A1R, A2AR and PDE10A collectively, and evaluation of their potential synergy in modulating cAMP levels.
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Affiliation(s)
- Leen Kalash
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Cristina Val
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jhonny Azuaje
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María I. Loza
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Fredrik Svensson
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB40WS UK
| | - Azedine Zoufir
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Lewis Mervin
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Discovery Sciences, AstraZeneca R&D, Cambridge Science Park, Cambridge, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB21QJ UK
| | - José Brea
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Robert Glen
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eddy Sotelo
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
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21
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Chen H, Bauer U, Engkvist O. Merged Multiple Ligands. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527674381.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hongming Chen
- Discovery Sciences, Innovative Medicines and Early Development; AstraZeneca; Pepparedsleden 1 431 83 Mölndal Sweden
| | - Udo Bauer
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development; AstraZeneca; Pepparedsleden 1 431 83 Mölndal Sweden
| | - Ola Engkvist
- Discovery Sciences, Innovative Medicines and Early Development; AstraZeneca; Pepparedsleden 1 431 83 Mölndal Sweden
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22
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El-Naggar AM, Abou-El-Regal MM, El-Metwally SA, Sherbiny FF, Eissa IH. Synthesis, characterization and molecular docking studies of thiouracil derivatives as potent thymidylate synthase inhibitors and potential anticancer agents. Mol Divers 2017; 21:967-983. [DOI: 10.1007/s11030-017-9776-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/02/2017] [Indexed: 11/27/2022]
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23
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Kumar A, Srivastava G, Srivastava S, Verma S, Negi AS, Sharma A. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease. J Mol Model 2017; 23:239. [PMID: 28741112 DOI: 10.1007/s00894-017-3396-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 12/11/2022]
Abstract
BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Swati Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Seema Verma
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Arvind S Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India.
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24
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Zhu M, Harshbarger WD, Robles O, Krysiak J, Hull KG, Cho SW, Richardson RD, Yang Y, Garcia A, Spiegelman L, Ramirez B, Wilson CT, Yau JA, Moore JT, Walker CB, Sacchettini JC, Liu WR, Sieber SA, Smith JW, Romo D. A strategy for dual inhibition of the proteasome and fatty acid synthase with belactosin C-orlistat hybrids. Bioorg Med Chem 2017; 25:2901-2916. [PMID: 28236510 PMCID: PMC5522751 DOI: 10.1016/j.bmc.2017.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/13/2017] [Indexed: 11/21/2022]
Abstract
The proteasome, a validated cellular target for cancer, is central for maintaining cellular homeostasis, while fatty acid synthase (FAS), a novel target for numerous cancers, is responsible for palmitic acid biosynthesis. Perturbation of either enzymatic machine results in decreased proliferation and ultimately cellular apoptosis. Based on structural similarities, we hypothesized that hybrid molecules of belactosin C, a known proteasome inhibitor, and orlistat, a known inhibitor of the thioesterase domain of FAS, could inhibit both enzymes. Herein, we describe proof-of-principle studies leading to the design, synthesis and enzymatic activity of several novel, β-lactone-based, dual inhibitors of these two enzymes. Validation of dual enzyme targeting through activity-based proteome profiling with an alkyne probe modeled after the most potent inhibitor, and preliminary serum stability studies of selected derivatives are also described. These results provide proof of concept for dual targeting of the proteasome and fatty acid synthase-thioesterase (FAS-TE) enabling a new approach for the development of drug-candidates with potential to overcome resistance.
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Affiliation(s)
- Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, TX 76706, USA
| | - Wayne D Harshbarger
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Omar Robles
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Joanna Krysiak
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, TX 76706, USA
| | - Sung Wook Cho
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | | | - Yanyan Yang
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Andres Garcia
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Lindsey Spiegelman
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Bianca Ramirez
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | | | - Ju Anne Yau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - James T Moore
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Caitlen B Walker
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Stephan A Sieber
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Jeffrey W Smith
- Sanford Burnham Medical Research Institute, La Jolla, CA, USA
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, TX 76706, USA.
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25
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Später T, Müller I, Eichler H, Menger MD, Laschke MW, Ampofo E. Dual inhibition of PI3K and mTOR by VS-5584 suppresses thrombus formation. Platelets 2017; 29:277-287. [PMID: 28503993 DOI: 10.1080/09537104.2017.1306040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
VS-5584 is a highly selective dual kinase inhibitor which suppresses phosphatidylinositol 3-kinase (PI3K) and mammalian target of rapamycin (mTOR) activity. Because these kinases are crucially involved in primary hemostasis, we herein investigated the effect of this compound on thrombus formation in vitro and in vivo. Pretreatment of washed platelets (WP) or platelet-rich plasma (PRP) with VS-5584 inhibited the agonist-induced activation of surface glycoprotein complex (GP)IIb/IIIa and the upregulation of P-selectin. This was associated with a significantly reduced formation of platelet-leukocyte aggregates (PLA). VS-5584 further attenuated platelet aggregation and adhesion after agonist stimulation. In contrast, endothelial expression of intercellular adhesion molecule (ICAM)-1 and vascular cellular adhesion molecule (VCAM)-1 and secretion of von Willebrand Factor (vWF) were not affected by the dual kinase inhibitor. In vivo, VS-5584 inhibited photochemically induced thrombus formation as shown by a significantly prolonged time to complete vessel occlusion when compared to vehicle-treated controls. This was associated with an elevated tail vein bleeding time, indicating a potential hemorrhagic risk in VS-5584-treated mice. Taken together, these novel findings demonstrate that VS-5584 is a potent inhibitor of primary hemostasis targeting multiple platelet functions.
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Affiliation(s)
- Thomas Später
- a Institute for Clinical & Experimental Surgery , Saarland University , Homburg/Saar , Germany
| | - Isabelle Müller
- b Institute for Hemostasiology & Transfusion Medicine , Saarland University , Homburg/Saar , Germany
| | - Hermann Eichler
- b Institute for Hemostasiology & Transfusion Medicine , Saarland University , Homburg/Saar , Germany
| | - Michael D Menger
- a Institute for Clinical & Experimental Surgery , Saarland University , Homburg/Saar , Germany
| | - Matthias W Laschke
- a Institute for Clinical & Experimental Surgery , Saarland University , Homburg/Saar , Germany
| | - Emmanuel Ampofo
- a Institute for Clinical & Experimental Surgery , Saarland University , Homburg/Saar , Germany
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26
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Designing multi-targeted agents: An emerging anticancer drug discovery paradigm. Eur J Med Chem 2017; 136:195-211. [PMID: 28494256 DOI: 10.1016/j.ejmech.2017.05.016] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 12/11/2022]
Abstract
The dominant paradigm in drug discovery is to design ligands with maximum selectivity to act on individual drug targets. With the target-based approach, many new chemical entities have been discovered, developed, and further approved as drugs. However, there are a large number of complex diseases such as cancer that cannot be effectively treated or cured only with one medicine to modulate the biological function of a single target. As simultaneous intervention of two (or multiple) cancer progression relevant targets has shown improved therapeutic efficacy, the innovation of multi-targeted drugs has become a promising and prevailing research topic and numerous multi-targeted anticancer agents are currently at various developmental stages. However, most multi-pharmacophore scaffolds are usually discovered by serendipity or screening, while rational design by combining existing pharmacophore scaffolds remains an enormous challenge. In this review, four types of multi-pharmacophore modes are discussed, and the examples from literature will be used to introduce attractive lead compounds with the capability of simultaneously interfering with different enzyme or signaling pathway of cancer progression, which will reveal the trends and insights to help the design of the next generation multi-targeted anticancer agents.
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27
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Leite FHA, Froes TQ, da Silva SG, de Souza EIM, Vital-Fujii DG, Trossini GHG, Pita SSDR, Castilho MS. An integrated approach towards the discovery of novel non-nucleoside Leishmania major pteridine reductase 1 inhibitors. Eur J Med Chem 2017; 132:322-332. [DOI: 10.1016/j.ejmech.2017.03.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/18/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
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28
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Toulouse JL, Abraham SMJ, Kadnikova N, Bastien D, Gauchot V, Schmitzer AR, Pelletier JN. Investigation of Classical Organic and Ionic Liquid Cosolvents for Early-Stage Screening in Fragment-Based Inhibitor Design with Unrelated Bacterial and Human Dihydrofolate Reductases. Assay Drug Dev Technol 2017; 15:141-153. [PMID: 28426233 DOI: 10.1089/adt.2016.768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug design by methods such as fragment screening requires effective solubilization of millimolar concentrations of small organic compounds while maintaining the properties of the biological target. We investigate four organic solvents and three 1-butyl-3-methylimidazolium (BMIm)-based ionic liquids (ILs) as cosolvents to establish conditions for screening two structurally unrelated dihydrofolate reductases (DHFRs) that are prime drug targets. Moderate concentrations (10%-15%) of cosolvents had little effect on inhibition of the microbial type II R67 DHFR and of human DHFR (hDHFR), while higher concentrations of organic cosolvents generally decreased activity of both DHFRs. In contrast, a specific IL conserved the activity of one DHFR, while severely reducing the activity of the other, and vice versa, illustrating the differing effect of ILs on distinct protein folds. Most of the cosolvents investigated preserved the fold of R67 DHFR and had little effect on binding of the cofactor NADPH, but reduced the productive affinity for its substrate. In contrast, cosolvents resulted in modest structural destabilization of hDHFR with little effect on productive affinity. We conclude that the organic cosolvents, methanol, dimethylformamide, and dimethylsulfoxide, offer the most balanced conditions for early-stage compound screening as they maintain sufficient biological activity of both DHFRs while allowing for compound dissolution in the millimolar range. However, IL cosolvents showed poor capacity to solubilize organic compounds at millimolar concentrations, mitigating their utility in early-stage screening. Nonetheless, ILs could provide an alternative to classical organic cosolvents when low concentrations of inhibitors are used, as when characterizing higher affinity inhibitors.
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Affiliation(s)
- Jacynthe L Toulouse
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Sarah M J Abraham
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Natalia Kadnikova
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Dominic Bastien
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Vincent Gauchot
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Andreea R Schmitzer
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Joelle N Pelletier
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
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Wang X, Zhang Y, Yang Y, Wu X, Fan H, Qiao Y. Identification of berberine as a direct thrombin inhibitor from traditional Chinese medicine through structural, functional and binding studies. Sci Rep 2017; 7:44040. [PMID: 28276481 PMCID: PMC5343495 DOI: 10.1038/srep44040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Thrombin acts as a key enzyme in the blood coagulation cascade and represents a potential drug target for the treatment of several cardiovascular diseases. The aim of this study was to identify small-molecule direct thrombin inhibitors from herbs used in traditional Chinese medicine (TCM). A pharmacophore model and molecular docking were utilized to virtually screen a library of chemicals contained in compositions of traditional Chinese herbs, and these analyses were followed by in vitro bioassay validation and binding studies. Berberine (BBR) was first confirmed as a thrombin inhibitor using an enzymatic assay. The BBR IC50 value for thrombin inhibition was 2.92 μM. Direct binding studies using surface plasmon resonance demonstrated that BBR directly interacted with thrombin with a KD value of 16.39 μM. Competitive binding assay indicated that BBR could bind to the same argartroban/thrombin interaction site. A platelet aggregation assay demonstrated that BBR had the ability to inhibit thrombin-induced platelet aggregation in washed platelets samples. This study proved that BBR is a direct thrombin inhibitor that has activity in inhibiting thrombin-induced platelet aggregation. BBR may be a potential candidate for the development of safe and effective thrombin-inhibiting drugs.
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Affiliation(s)
- Xing Wang
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, 6 Central Ring South Road, Wangjing, Beijing 100102, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Xia Wu
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Hantian Fan
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Yanjiang Qiao
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, 6 Central Ring South Road, Wangjing, Beijing 100102, China
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30
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Lou Y, Wang Q, Zheng J, Hu H, Liu L, Hong D, Zeng S. Possible Pathways of Capecitabine-Induced Hand–Foot Syndrome. Chem Res Toxicol 2016; 29:1591-1601. [PMID: 27631426 DOI: 10.1021/acs.chemrestox.6b00215] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yan Lou
- The
First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People’s Republic of China
| | - Qian Wang
- The
First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People’s Republic of China
| | - Jinqi Zheng
- Zhejiang Institute for Food and Drug Control, Hangzhou, Zhejiang 310004, People’s Republic of China
| | - Haihong Hu
- Laboratory
of Pharmaceutical Analysis and Drug Metabolism, Zhejiang Province
Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical
Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People’s Republic of China
| | - Lin Liu
- The
First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People’s Republic of China
| | - Dongsheng Hong
- The
First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People’s Republic of China
| | - Su Zeng
- Laboratory
of Pharmaceutical Analysis and Drug Metabolism, Zhejiang Province
Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical
Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People’s Republic of China
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31
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Discovery of Dual ETA/ETB Receptor Antagonists from Traditional Chinese Herbs through in Silico and in Vitro Screening. Int J Mol Sci 2016; 17:389. [PMID: 26999111 PMCID: PMC4813245 DOI: 10.3390/ijms17030389] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/25/2016] [Accepted: 03/04/2016] [Indexed: 11/30/2022] Open
Abstract
Endothelin-1 receptors (ETAR and ETBR) act as a pivotal regulator in the biological effects of ET-1 and represent a potential drug target for the treatment of multiple cardiovascular diseases. The purpose of the study is to discover dual ETA/ETB receptor antagonists from traditional Chinese herbs. Ligand- and structure-based virtual screening was performed to screen an in-house database of traditional Chinese herbs, followed by a series of in vitro bioassay evaluation. Aristolochic acid A (AAA) was first confirmed to be a dual ETA/ETB receptor antagonist based intracellular calcium influx assay and impedance-based assay. Dose-response curves showed that AAA can block both ETAR and ETBR with IC50 of 7.91 and 7.40 μM, respectively. Target specificity and cytotoxicity bioassay proved that AAA is a selective dual ETA/ETB receptor antagonist and has no significant cytotoxicity on HEK293/ETAR and HEK293/ETBR cells within 24 h. It is a feasible and effective approach to discover bioactive compounds from traditional Chinese herbs using in silico screening combined with in vitro bioassay evaluation. The structural characteristic of AAA for its activity was especially interpreted, which could provide valuable reference for the further structural modification of AAA.
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Rahman A, Hoque MM, Khan MAK, Sarwar MG, Halim MA. Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach. SPRINGERPLUS 2016; 5:146. [PMID: 27026843 PMCID: PMC4764604 DOI: 10.1186/s40064-016-1844-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/15/2016] [Indexed: 11/10/2022]
Abstract
Capecitabine, a fluoropyrimidine prodrug, has been a frequently chosen ligand for the last one and half decades to inhibit thymidylate synthase (TYMS) for treatment of colorectal cancer. TYMS is a key enzyme for de novo synthesis of deoxythymidine monophosphate and subsequent synthesis of DNA. Recent years have also seen the trait of modifying ligands using halogens and trifluoromethyl (–CF3) group to ensure enhanced drug performance. In this study, in silico modification of capecitabine with Cl, Br, I atoms and –CF3 group has been performed. Density functional theory has been employed to optimize the drug molecules and elucidate their thermodynamic and electrical properties such as Gibbs free energy, enthalpy, electronic energy, dipole moment and frontier orbital features (HOMO–LUMO gap, hardness and softness). Flexible and rigid molecular docking have been implemented between drugs and the receptor TYMS. Both inter- and intra-molecular non-covalent interactions involving the amino acid residues of TYMS and the drug molecules are explored in details. The drugs were superimposed on the resolved crystal structure (at 1.9 Å) of ZD1694/dUMP/TYMS system to shed light on similarity of the binding of capecitabine, and its modifiers, to that of ZD1694. Together, these results may provide more insights prior to synthesizing halogen-directed derivatives of capecitabine for anticancer treatment.
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Affiliation(s)
- Adhip Rahman
- Bangladesh Institute of Computational Chemistry and Biochemistry, 38 Green Road West, Dhaka, 1205 Bangladesh ; Department of Chemistry, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Mohammad Mazharol Hoque
- Bangladesh Institute of Computational Chemistry and Biochemistry, 38 Green Road West, Dhaka, 1205 Bangladesh
| | - Mohammad A K Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961 The Kingdom of Saudi Arabia
| | - Mohammed G Sarwar
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, MB26, La Jolla, CA 92037 USA
| | - Mohammad A Halim
- Bangladesh Institute of Computational Chemistry and Biochemistry, 38 Green Road West, Dhaka, 1205 Bangladesh ; Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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Musso L, Dallavalle S, Zunino F. Perspectives in the development of hybrid bifunctional antitumour agents. Biochem Pharmacol 2015; 96:297-305. [DOI: 10.1016/j.bcp.2015.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/05/2015] [Indexed: 01/04/2023]
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Liargkova T, Hadjipavlou-Litina DJ, Koukoulitsa C, Voulgari E, Avgoustakis C. Simple chalcones and bis-chalcones ethers as possible pleiotropic agents. J Enzyme Inhib Med Chem 2015; 31:302-13. [PMID: 25798685 DOI: 10.3109/14756366.2015.1021253] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The synthesis, the antioxidative properties and the lipoxygenase (LOX) and acetylcholinesterase (AChE) inhibition of a number of 4-hydroxy-chalcones diversely substituted as well as of a series of bis-chalcones ether derivatives are reported. The chalcones derivatives were readily produced using a Claisen-Schmidt condensation in a ultra sound bath in good yields. The structures of the synthesized compounds were confirmed by spectral and elemental analysis. Their lipophilicity is experimentally determined by reversed-phase thin-layer chromatography method. Most of them are potent in vitro inhibitors of lipid peroxidation and of LOX. Compounds b2 and b3 were found to be the most potent LOX and AChE inhibitors among the tested derivatives with a significant anti-lipid peroxidation profile. The results led us to propose these enone derivatives as new multifunctional compounds against Alzheimer's disease. The results are discussed in terms of structural and physicochemical characteristics of the compounds. Moreover, the pharmacokinetic profile of these compounds was investigated using computational methods.
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Affiliation(s)
- Thalia Liargkova
- a Department of Pharmaceutical Chemistry , School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Dimitra J Hadjipavlou-Litina
- a Department of Pharmaceutical Chemistry , School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Caterina Koukoulitsa
- b Chemistry Department, University of Athens , Panepistimiopolis-Zografou , Greece , and
| | - Efstathia Voulgari
- c Department of Pharmaceutical Technology and Pharmaceutical Analysis , School of Pharmacy, University of Patras , Rio Patras , Greece
| | - Constantinos Avgoustakis
- c Department of Pharmaceutical Technology and Pharmaceutical Analysis , School of Pharmacy, University of Patras , Rio Patras , Greece
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Theoretical approaches to identify the potent scaffold for human sirtuin1 activator: Bayesian modeling and density functional theory. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0983-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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