1
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Li Y, Zhang Y, Zhang J, Zhan Z, Mao W. Development of novel focal adhesion kinase (FAK) inhibitors for targeting cancer: Structural insights and therapeutic potential. Eur J Med Chem 2024; 279:116913. [PMID: 39357313 DOI: 10.1016/j.ejmech.2024.116913] [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: 08/23/2024] [Revised: 09/18/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase frequently overexpressed in various cancer cells, facilitating tumor growth through the regulation of cell adhesion, migration, and proliferation. Consequently, targeting FAK is considered a promising anti-tumor strategy, particularly for invasive cancers. Numerous potent small-molecule inhibitors have progressed to clinical trials. Among these, Defactinib is under evaluation for regulatory approval as a treatment for ovarian serous tumors. Furthermore, novel FAK inhibitors, including PROTACs, have emerged as key research focuses, anticipated to overcome the limitations of traditional inhibitors. In this Perspective, we highlight the protein structure, biological functions, relevant signaling pathways, and associations of FAK with cancer development. We also analyze the clinical status of FAK inhibitors, paying special attention to the various classes of FAK inhibitors, with detailed analyses of their chemical structures, structure-activity relationships (SARs), bioactivity profiles, selectivity profiles, and therapeutic potentials.
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Affiliation(s)
- Yingnan Li
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Neuro-system and Multimorbidity Laboratory, State Key Laboratory of Biotherapy and Cancer Center and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, 610041, Sichuan, China
| | - Yuming Zhang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Neuro-system and Multimorbidity Laboratory, State Key Laboratory of Biotherapy and Cancer Center and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, 610041, Sichuan, China; West China College of Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Neuro-system and Multimorbidity Laboratory, State Key Laboratory of Biotherapy and Cancer Center and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, 610041, Sichuan, China
| | - Zixuan Zhan
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Neuro-system and Multimorbidity Laboratory, State Key Laboratory of Biotherapy and Cancer Center and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, 610041, Sichuan, China.
| | - Wuyu Mao
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Neuro-system and Multimorbidity Laboratory, State Key Laboratory of Biotherapy and Cancer Center and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, 610041, Sichuan, China.
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2
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Tolbatov I, Umari P, Marrone A. The binding of diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes at DNA/RNA nucleobases: Computational evidences of an appreciable selectivity toward the AU base pairs. J Mol Graph Model 2024; 131:108806. [PMID: 38824876 DOI: 10.1016/j.jmgm.2024.108806] [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: 02/20/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Multiple medicinal strategies involve modifications of the structure of DNA or RNA, which disrupt their correct functioning. Metal complexes with medicinal effects, also known as metallodrugs, are among the agents intended specifically for the attack onto nucleosides. The diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes constitute promising dual acting drugs due to their ability to release the therapeutically active bridging ligands upon their substitution by endogenous ligands. In this paper, we study the structure and the stability of the complexes formed by the diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes coordinated in axial positions with the DNA/RNA nucleobases or base pairs, assuming the attainable metalation at all the accessible pyridyl nitrogens. Dirhodium complexes coordinate at the pyridyl nitrogens more strongly than the diruthenium complexes. On the other hand, we found that the diruthenium scaffold binds more selectively to nucleobase targets. Furthermore, we reveal a tighter coordination of diruthenium complex at the adenine-uracil base pair, compared to adenine-thymine, hence constituting a scarce instance of RNA-selectivity. We envision that the here reported computational outcomes may pace future experiments addressing the binding of diruthenium and dirhodium paddlewheel complexes at either single nucleobases or DNA/RNA fragments.
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Affiliation(s)
- Iogann Tolbatov
- Department of Physics and Astronomy, University of Padova, via F. Marzolo 8, 35131, Padova, Italy.
| | - Paolo Umari
- Department of Physics and Astronomy, University of Padova, via F. Marzolo 8, 35131, Padova, Italy
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy
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3
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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4
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Yu B, Bolik-Coulon N, Rangadurai AK, Kay LE, Iwahara J. Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules. J Am Chem Soc 2024; 146:20788-20801. [PMID: 39028837 PMCID: PMC11295196 DOI: 10.1021/jacs.4c04433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/09/2024] [Accepted: 06/28/2024] [Indexed: 07/21/2024]
Abstract
NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of 1H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (ϕENS) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ϕENS values and demonstrate its utility through applications to a number of biomolecular systems. The use of Gd-based cosolutes offers several advantages over nitroxides for ϕENS measurements. First, unlike nitroxide compounds, Gd chelates enable electrostatic potential measurements on oxidation-sensitive proteins that require reducing agents. Second, the large electron spin quantum number of Gd (7/2) results in notably larger PREs for Gd chelates when used at the same concentrations as nitroxide radicals. Thus, it is possible to measure ϕENS values exclusively from + and - charged compounds even for highly charged biomolecules, avoiding the use of neutral cosolutes that, as we further establish here, limits the accuracy of the measured electrostatic potentials. In addition, the smaller concentrations of cosolutes required minimize potential binding to sites on macromolecules. Fourth, the closer proximity of the paramagnetic center and charged groups within Gd chelates, in comparison to the corresponding nitroxide compounds, enables more accurate predictions of ϕENS potentials for cross-validation of the experimental results. The Gd-based method described here, thus, broadens the applicability of studies of biomolecular electrostatics using solution NMR spectroscopy.
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Affiliation(s)
- Binhan Yu
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Nicolas Bolik-Coulon
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Atul K. Rangadurai
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Lewis E. Kay
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Junji Iwahara
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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5
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Gedgaudas M, Kaziukonytė P, Kairys V, Mickevičiūtė A, Zubrienė A, Brukštus A, Matulis D, Kazlauskas E. Comprehensive analysis of resorcinyl-imidazole Hsp90 inhibitor design. Eur J Med Chem 2024; 273:116505. [PMID: 38788300 DOI: 10.1016/j.ejmech.2024.116505] [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: 03/05/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Human Hsp90 chaperones are implicated in various aspects of cancer. Due to this, Hsp90 has been explored as potential target in cancer treatment. Initial attempts to use Hsp90 inhibitors in drug trials failed due to toxicity and inefficacy. The next generation of drugs were less toxic but still insufficiently effective in a clinical setting. Recently, a lot of effort is being put into understanding the consequences of Hsp90 isoform selective inhibition, expecting that this might hold the key in targeting Hsp90 for disease treatment. Here we investigate a series of compounds containing the aryl-resorcinol scaffold with a 5-membered ring as a promising class of new human Hsp90 inhibitors, reaching nanomolar affinity. We compare how the replacement of 5-membered ring, from thiadiazole to imidazole, as well as a variety of their substituents, influences the potency of these inhibitors for Hsp90 alpha and beta isoforms. To further elucidate the dissimilarity in ligand selectivity between the isoforms, a mutant protein was constructed and tested against the ligand library. In addition, we performed a series of molecular dynamics (MD) and docking simulations to further explain our experimental findings as well as evaluated key compounds in cell assays. Our results deepen the understanding of Hsp90 isoform ligand selectivity and serve as an informative base for further Hsp90 inhibitor optimization.
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Affiliation(s)
- Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Paulina Kaziukonytė
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Algirdas Brukštus
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
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6
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Chayka A, Česnek M, Kužmová E, Kozák J, Tloušt'ová E, Dvořáková A, Strmeň T, Brož B, Osifová Z, Dračínský M, Mertlíková-Kaiserová H, Janeba Z. Structure-Based Drug Design of ADRA2A Antagonists Derived from Yohimbine. J Med Chem 2024; 67:10135-10151. [PMID: 38857067 PMCID: PMC11215778 DOI: 10.1021/acs.jmedchem.4c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/29/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Yohimbine, a natural indole alkaloid and a nonselective adrenoceptor antagonist, possesses potential benefits in treating inflammatory disorders and sepsis. Nevertheless, its broader clinical use faces challenges due to its low receptor selectivity. A structure-activity relationship study of novel yohimbine analogues identified amino esters of yohimbic acid as potent and selective ADRA2A antagonists. Specifically, amino ester 4n, in comparison to yohimbine, showed a 6-fold higher ADRA1A/ADRA2A selectivity index (SI > 556 for 4n) and a 25-fold higher ADRA2B/ADRA2A selectivity index. Compound 4n also demonstrated high plasma and microsomal stability, moderate-to-low membrane permeability determining its limited ability to cross the blood-brain barrier, and negligible toxicity on nontumor normal human dermal fibroblasts. Compound 4n represents an important complementary pharmacological tool to study the involvement of adrenoceptor subtypes in pathophysiologic conditions such as inflammation and sepsis and a novel candidate for further preclinical development to treat ADRA2A-mediated pathologies.
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Affiliation(s)
- Artem Chayka
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Michal Česnek
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Jaroslav Kozák
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Eva Tloušt'ová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Timotej Strmeň
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Břetislav Brož
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Zuzana Osifová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
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7
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Dziduch K, Janowska S, Andrzejczuk S, Strzyga-Łach P, Struga M, Feldo M, Demchuk O, Wujec M. Synthesis and Biological Evaluation of New Compounds with Nitroimidazole Moiety. Molecules 2024; 29:3023. [PMID: 38998972 PMCID: PMC11243693 DOI: 10.3390/molecules29133023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Heterocyclic compounds, particularly those containing azole rings, have shown extensive biological activity, including anticancer, antibacterial, and antifungal properties. Among these, the imidazole ring stands out due to its diverse therapeutic potential. In the presented study, we designed and synthesized a series of imidazole derivatives to identify compounds with high biological potential. We focused on two groups: thiosemicarbazide derivatives and hydrazone derivatives. We synthesized these compounds using conventional methods and confirmed their structures via nuclear magnetic resonance spectroscopy (NMR), MS, and elemental analysis, and then assessed their antibacterial and antifungal activities in vitro using the broth microdilution method against Gram-positive and Gram-negative bacteria, as well as Candida spp. strains. Our results showed that thiosemicarbazide derivatives exhibited varied activity against Gram-positive bacteria, with MIC values ranging from 31.25 to 1000 µg/mL. The hydrazone derivatives, however, did not display significant antibacterial activity. These findings suggest that structural modifications can significantly influence the antimicrobial efficacy of imidazole derivatives, highlighting the potential of thiosemicarbazide derivatives as promising candidates for further development in antibacterial therapies. Additionally, the cytotoxic activity against four cancer cell lines was evaluated. Two derivatives of hydrazide-hydrazone showed moderate anticancer activity.
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Affiliation(s)
- Katarzyna Dziduch
- Doctoral School, Medical University of Lublin, Chodzki 7, 20-093 Lublin, Poland
| | - Sara Janowska
- Department of Pathobiochemistry and Interdisciplinary Applications of Ion Chromatography, Biomedical Sciences, Medical University of Lublin, 1 Chodzki Street, 20-093 Lublin, Poland
| | - Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University, 20-093 Lublin, Poland
| | - Paulina Strzyga-Łach
- Chair and Department of Biochemistry, Medical University of Warsaw, 02-097 Warszawa, Poland
| | - Marta Struga
- Chair and Department of Biochemistry, Medical University of Warsaw, 02-097 Warszawa, Poland
| | - Marcin Feldo
- Department of Vascular Surgery, Medical University of Lublin, Staszica 11 St., 20-081 Lublin, Poland
| | - Oleg Demchuk
- Faculty of Medicine, The John Paul II Catholic University of Lublin, Konstantynow 1J, 20-708 Lublin, Poland
| | - Monika Wujec
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki Street, 20-093 Lublin, Poland
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8
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Revanasiddappa PD, Gowtham HG, G. S. C, Gangadhar S, A. S, Murali M, Shivamallu C, Achar RR, Silina E, Stupin V, Manturova N, Shati AA, Alfaifi MY, Elbehairi SEI, Kollur SP, Amruthesh KN. Exploration of Type III effector Xanthomonas outer protein Q (XopQ) inhibitor from Picrasma quassioides as an antibacterial agent using chemoinformatics analysis. PLoS One 2024; 19:e0302105. [PMID: 38889115 PMCID: PMC11185476 DOI: 10.1371/journal.pone.0302105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
The present study was focused on exploring the efficient inhibitors of closed state (form) of type III effector Xanthomonas outer protein Q (XopQ) (PDB: 4P5F) from the 44 phytochemicals of Picrasma quassioides using cutting-edge computational analysis. Among them, Kumudine B showed excellent binding energy (-11.0 kcal/mol), followed by Picrasamide A, Quassidine I and Quassidine J with the targeted closed state of XopQ protein compared to the reference standard drug (Streptomycin). The molecular dynamics (MD) simulations performed at 300 ns validated the stability of top lead ligands (Kumudine B, Picrasamide A, and Quassidine I)-bound XopQ protein complex with slightly lower fluctuation than Streptomycin. The MM-PBSA calculation confirmed the strong interactions of top lead ligands (Kumudine B and QuassidineI) with XopQ protein, as they offered the least binding energy. The results of absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis confirmed that Quassidine I, Kumudine B and Picrasamide A were found to qualify most of the drug-likeness rules with excellent bioavailability scores compared to Streptomycin. Results of the computational studies suggested that Kumudine B, Picrasamide A, and Quassidine I could be considered potential compounds to design novel antibacterial drugs against X. oryzae infection. Further in vitro and in vivo antibacterial activities of Kumudine B, Picrasamide A, and Quassidine I are required to confirm their therapeutic potentiality in controlling the X. oryzae infection.
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Affiliation(s)
| | - H. G. Gowtham
- Department of Studies and Research in Food Science and Nutrition, KSOU, Mysuru, Karnataka, India
| | - Chikkanna G. S.
- Department of Home Science, ICAR Krishi Vigyan Kendra, Kolar, India
| | - Suchithra Gangadhar
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Satish A.
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - M. Murali
- Department of Studies in Botany, University of Mysore, Mysuru, Karnataka, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Manturova
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Serag Eldin I. Elbehairi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka, India
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9
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Kudo G, Hirao T, Harada R, Hirokawa T, Shigeta Y, Yoshino R. Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation. Sci Rep 2024; 14:13508. [PMID: 38866895 PMCID: PMC11169543 DOI: 10.1038/s41598-024-64236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor was developed that mimics S-adenosyl-l-methionine and deoxycytidine; however, the mechanism of selectivity is unclear because the inhibitor-protein complex structure determination is absent. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning showed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as evidenced by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures.
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Affiliation(s)
- Genki Kudo
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Takumi Hirao
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yasuteru Shigeta
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryunosuke Yoshino
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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10
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Mogire RM, Miruka SA, Juma DW, McNamara CW, Andagalu B, Burrows JN, Chenu E, Duffy J, Ogutu BR, Akala HM. Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum. J Cheminform 2024; 16:63. [PMID: 38831351 PMCID: PMC11145868 DOI: 10.1186/s13321-024-00856-7] [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: 11/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it is possible to predict compounds' activity and identify their potential targets across diverse organisms. In this study, we aimed to assess the antiplasmodial activity of compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library using in vitro and bioinformatics approaches. We assessed the in vitro antiplasmodial activity of the compounds using blood-stage and liver-stage drug susceptibility assays. We used protein sequences of known targets of the ReFRAME compounds with high antiplasmodial activity (EC50 < 10 uM) to conduct a protein-pairwise search to identify similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) using NCBI protein BLAST. We further assessed the association between the compounds' in vitro antiplasmodial activity and level of similarity between their known and predicted P. falciparum target proteins using simple linear regression analyses. BLAST analyses revealed 735 P. falciparum proteins that were similar to the 226 known protein targets associated with the ReFRAME compounds. Antiplasmodial activity of the compounds was positively associated with the degree of similarity between the compounds' known targets and predicted P. falciparum protein targets (percentage identity, E value, and bit score), the number of the predicted P. falciparum targets, and their respective mutagenesis index and fitness scores (R2 between 0.066 and 0.92, P < 0.05). Compounds predicted to target essential P. falciparum proteins or those with a druggability index of 1 showed the highest antiplasmodial activity.
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Affiliation(s)
- Reagan M Mogire
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
| | - Silviane A Miruka
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Dennis W Juma
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicine, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Andagalu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
| | | | - Elodie Chenu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Bernhards R Ogutu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Hoseah M Akala
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya.
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11
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. Int J Mol Sci 2024; 25:5368. [PMID: 38791406 PMCID: PMC11121299 DOI: 10.3390/ijms25105368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The allosteric inhibition of insulin-like growth factor receptor 1 kinase (IGF1RK) is a potential strategy to overcome selectivity barriers for targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives that have been reported as allosteric inhibitors of IGF1RK. We further studied the dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation: forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen-bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the positioning of chemical substituents with different pharmacophore features at the R1 indole ring influences molecular interactions and binding conformations of indole-butyl-amine derivatives and, hence, dramatically affects their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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12
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Burger PB, Hu X, Balabin I, Muller M, Stanley M, Joubert F, Kaiser TM. FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. J Chem Inf Model 2024; 64:3812-3825. [PMID: 38651738 PMCID: PMC11094716 DOI: 10.1021/acs.jcim.4c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. In recent years, two computational techniques, machine learning (ML) and physics-based methods, have evolved substantially and are now frequently incorporated into the medicinal chemist's toolbox to enhance the efficiency of both hit optimization and candidate design. Both computational methods come with their own set of limitations, and they are often used independently of each other. ML's capability to screen extensive compound libraries expediently is tempered by its reliance on quality data, which can be scarce especially during early-stage optimization. Contrarily, physics-based approaches like free energy perturbation (FEP) are frequently constrained by low throughput and high cost by comparison; however, physics-based methods are capable of making highly accurate binding affinity predictions. In this study, we harnessed the strength of FEP to overcome data paucity in ML by generating virtual activity data sets which then inform the training of algorithms. Here, we show that ML algorithms trained with an FEP-augmented data set could achieve comparable predictive accuracy to data sets trained on experimental data from biological assays. Throughout the paper, we emphasize key mechanistic considerations that must be taken into account when aiming to augment data sets and lay the groundwork for successful implementation. Ultimately, the study advocates for the synergy of physics-based methods and ML to expedite the lead optimization process. We believe that the physics-based augmentation of ML will significantly benefit drug discovery, as these techniques continue to evolve.
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Affiliation(s)
- Pieter B. Burger
- Avicenna
Biosciences Inc., 101
W. Chapel Hill Street, Suite 210, Durham, North Carolina 27001, United States
| | - Xiaohu Hu
- Schrödinger,
Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ilya Balabin
- Avicenna
Biosciences Inc., 101
W. Chapel Hill Street, Suite 210, Durham, North Carolina 27001, United States
| | - Morné Muller
- Avicenna
Biosciences Inc., 101
W. Chapel Hill Street, Suite 210, Durham, North Carolina 27001, United States
| | - Megan Stanley
- Microsoft
Research AI4Science, 21 Station Road, Cambridge CB1 2FB, U.K.
| | - Fourie Joubert
- Centre
for Bioinformatics and Computational Biology, Department of Biochemistry,
Genetics and Microbiology, University of
Pretoria, Pretoria 0001, South Africa
| | - Thomas M. Kaiser
- Avicenna
Biosciences Inc., 101
W. Chapel Hill Street, Suite 210, Durham, North Carolina 27001, United States
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13
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588115. [PMID: 38617226 PMCID: PMC11014618 DOI: 10.1101/2024.04.04.588115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The allosteric inhibition of Insulin-like Growth Factor Receptor 1 Kinase (IGF1RK) is a potential strategy to overcome selectivity barriers in targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives which have been reported as allosteric inhibitors of IGF1RK. We further studied dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation, forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the position of chemical substituents at the R1 indole ring with different pharmacophore features influences molecular interactions and binding conformations of the indole-butyl-amine derivatives, hence dramatically affecting their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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14
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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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15
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Zhao Y, Zhao X, Duan L, Hou R, Gu Y, Liu Z, Chen J, Wu F, Yang L, Le XC, Wang Q, Yan X. Reinvent Aliphatic Arsenicals as Reversible Covalent Warheads toward Targeted Kinase Inhibition and Non-acute Promyelocytic Leukemia Cancer Treatment. J Med Chem 2024; 67:5458-5472. [PMID: 38556750 DOI: 10.1021/acs.jmedchem.3c02076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The success of arsenic in acute promyelocytic leukemia (APL) treatment is hardly transferred to non-APL cancers, mainly due to the low selectivity and weak binding affinity of traditional arsenicals to oncoproteins critical for cancer survival. We present herein the reinvention of aliphatic trivalent arsenicals (As) as reversible covalent warheads of As-based targeting inhibitors toward Bruton's tyrosine kinase (BTK). The effects of As warheads' valency, thiol protection, methylation, spacer length, and size on inhibitors' activity were studied. We found that, in contrast to the bulky and rigid aromatic As warhead, the flexible aliphatic As warheads were well compatible with the well-optimized guiding group to achieve nanomolar inhibition against BTK. The optimized As inhibitors effectively blocked the BTK-mediated oncogenic signaling pathway, leading to elevated antiproliferative activities toward lymphoma cells and xenograft tumor. Our study provides a promising strategy enabling rational design of new aliphatic arsenic-based reversible covalent inhibitors toward non-APL cancer treatment.
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Affiliation(s)
- Yang Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinyue Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lewei Duan
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
| | - Ruxue Hou
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuxin Gu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Liu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianbin Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Feizhen Wu
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Limin Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaowen Yan
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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16
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Li Z, Shao Y, Yang Y, Zan J. Zeolitic imidazolate framework-8: a versatile nanoplatform for tissue regeneration. Front Bioeng Biotechnol 2024; 12:1386534. [PMID: 38655386 PMCID: PMC11035894 DOI: 10.3389/fbioe.2024.1386534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
Extensive research on zeolitic imidazolate framework (ZIF-8) and its derivatives has highlighted their unique properties in nanomedicine. ZIF-8 exhibits advantages such as pH-responsive dissolution, easy surface functionalization, and efficient drug loading, making it an ideal nanosystem for intelligent drug delivery and phototherapy. These characteristics have sparked significant interest in its potential applications in tissue regeneration, particularly in bone, skin, and nerve regeneration. This review provides a comprehensive assessment of ZIF-8's feasibility in tissue engineering, encompassing material synthesis, performance testing, and the development of multifunctional nanosystems. Furthermore, the latest advancements in the field, as well as potential limitations and future prospects, are discussed. Overall, this review emphasizes the latest developments in ZIF-8 in tissue engineering and highlights the potential of its multifunctional nanoplatforms for effective complex tissue repair.
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Affiliation(s)
- Zhixin Li
- Department of Rehabilitation, Ganzhou People’s Hospital, Ganzhou, China
| | - Yinjin Shao
- Department of Rehabilitation, Ganzhou People’s Hospital, Ganzhou, China
| | - Youwen Yang
- Institute of Additive Manufacturing, Jiangxi University of Science and Technology, Nanchang, China
| | - Jun Zan
- Institute of Additive Manufacturing, Jiangxi University of Science and Technology, Nanchang, China
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17
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Tu G, Fu T, Zheng G, Xu B, Gou R, Luo D, Wang P, Xue W. Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J Chem Inf Model 2024; 64:1433-1455. [PMID: 38294194 DOI: 10.1021/acs.jcim.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Binbin Xu
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610200, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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18
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Selvaraj C, Pedone E, Lee JK, Singh SK. Editorial: Molecular level atomistic and structural insights on biological macromolecules, inhibition, and dynamics studies. Front Mol Biosci 2024; 11:1362215. [PMID: 38516195 PMCID: PMC10955358 DOI: 10.3389/fmolb.2024.1362215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Chandrabose Selvaraj
- Computational and Structural Research in Drug Discovery Lab (CSRDD), Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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19
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Zeng S, Wu M, Jin Y, Ye Y, Xia H, Chen X, Che J, Wang Z, Wu Y, Dong X, Chen Y, Huang W. Discovery of novel, potent, selective and orally bioavailable HPK1 inhibitor for enhancing the efficacy of anti-PD-L1 antibody. Eur J Med Chem 2024; 267:116206. [PMID: 38350360 DOI: 10.1016/j.ejmech.2024.116206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/15/2024]
Abstract
Hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase in the MAP4K family, is expressed predominantly in immune cells, and has been identified as a negative regulator of immune signaling. Accumulating evidences demonstrated that loss of HPK1 kinase function effectively enhances anti-tumor responses. In this study, we disclose the medicinal chemistry campaigns to discovery potent, selective, and orally active HPK1 inhibitors, starting from our previous work based on rigidification strategy. Systematically structure-activity relationship (SAR) exploration led to the identification of F03 (HMC-B17). The representative compound, HMC-B17, showed the potent HPK1 inhibition with an IC50 value of 1.39 nM and favorable selectivity against TCR-related kinases. In addition, the HMC-B17 effectively enhanced the IL-2 secretion in Jurkat cells (EC50 = 11.56 nM). Strikingly, immune-reverse effects and improved immune response in vivo were observed after HMC-B17 treatment. Furthermore, HMC-B17 combined with anti-PD-L1 antibody demonstrated a synergistic antitumor efficacy with TGI% value of 71.24 % in CT26 model. Collectively, our findings suggest that HMC-B17 could be a valuable lead compound to develop a safe and potent HPK1 inhibitor for further cancer immunotherapy.
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Affiliation(s)
- Shenxin Zeng
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China.
| | - Mingfei Wu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yuyuan Jin
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China
| | - Yingqiao Ye
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China
| | - Heye Xia
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China
| | - Xinyi Chen
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Zunyuan Wang
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China
| | - Ying Wu
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| | - Yinqiao Chen
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China.
| | - Wenhai Huang
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, PR China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, PR China.
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20
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Hermosilla M. Regulating ethical experimentation: Impacts of the breakthrough therapy designation on drug R&D. JOURNAL OF HEALTH ECONOMICS 2024; 94:102855. [PMID: 38241795 DOI: 10.1016/j.jhealeco.2023.102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024]
Abstract
This article investigates patterns of pharmaceutical development activity around the 2012 creation of the FDA's Breakthrough Therapy Designation (BTD). The BTD introduced regulatory flexibility and support to avoid ethical challenges created by experimental therapies of exceptional performance in early stage clinical trials. We argue that the program's design indirectly created substantial incentives for the industry to pursue the designation. Consistent with this hypothesis, our evidence links the creation of the program with a substantial increase in the number of new drug indications entering the clinical trial process. This surge in introductions has resulted in a discernible increase in approvals, which has manifested with a lag and may strengthen in the future. Countering theoretical predictions, BTD incentives have not led to increased risk taking in project selection.
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Affiliation(s)
- Manuel Hermosilla
- University of Illinois at Chicago, College of Business Administration, United States of America; Johns Hopkins University, Carey Business School, United States of America.
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21
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Cichońska A, Ravikumar B, Rahman R. AI for targeted polypharmacology: The next frontier in drug discovery. Curr Opin Struct Biol 2024; 84:102771. [PMID: 38215530 DOI: 10.1016/j.sbi.2023.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024]
Abstract
In drug discovery, targeted polypharmacology, i.e., targeting multiple molecular targets with a single drug, is redefining therapeutic design to address complex diseases. Pre-selected pharmacological profiles, as exemplified in kinase drugs, promise enhanced efficacy and reduced toxicity. Historically, many of such drugs were discovered serendipitously, limiting predictability and efficacy, but currently artificial intelligence (AI) offers a transformative solution. Machine learning and deep learning techniques enable modeling protein structures, generating novel compounds, and decoding their polypharmacological effects, opening an avenue for more systematic and predictive multi-target drug design. This review explores the use of AI in identifying synergistic co-targets and delineating them from anti-targets that lead to adverse effects, and then discusses advances in AI-enabled docking, generative chemistry, and proteochemometric modeling of proteome-wide compound interactions, in the context of polypharmacology. We also provide insights into challenges ahead.
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22
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Shehjar F, Almarghalani DA, Mahajan R, Hasan SAM, Shah ZA. The Multifaceted Role of Cofilin in Neurodegeneration and Stroke: Insights into Pathogenesis and Targeting as a Therapy. Cells 2024; 13:188. [PMID: 38247879 PMCID: PMC10814918 DOI: 10.3390/cells13020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
This comprehensive review explores the complex role of cofilin, an actin-binding protein, across various neurodegenerative diseases (Alzheimer's, Parkinson's, schizophrenia, amyotrophic lateral sclerosis (ALS), Huntington's) and stroke. Cofilin is an essential protein in cytoskeletal dynamics, and any dysregulation could lead to potentially serious complications. Cofilin's involvement is underscored by its impact on pathological hallmarks like Aβ plaques and α-synuclein aggregates, triggering synaptic dysfunction, dendritic spine loss, and impaired neuronal plasticity, leading to cognitive decline. In Parkinson's disease, cofilin collaborates with α-synuclein, exacerbating neurotoxicity and impairing mitochondrial and axonal function. ALS and frontotemporal dementia showcase cofilin's association with genetic factors like C9ORF72, affecting actin dynamics and contributing to neurotoxicity. Huntington's disease brings cofilin into focus by impairing microglial migration and influencing synaptic plasticity through AMPA receptor regulation. Alzheimer's, Parkinson's, and schizophrenia exhibit 14-3-3 proteins in cofilin dysregulation as a shared pathological mechanism. In the case of stroke, cofilin takes center stage, mediating neurotoxicity and neuronal cell death. Notably, there is a potential overlap in the pathologies and involvement of cofilin in various diseases. In this context, referencing cofilin dysfunction could provide valuable insights into the common pathologies associated with the aforementioned conditions. Moreover, this review explores promising therapeutic interventions, including cofilin inhibitors and gene therapy, demonstrating efficacy in preclinical models. Challenges in inhibitor development, brain delivery, tissue/cell specificity, and long-term safety are acknowledged, emphasizing the need for precision drug therapy. The call to action involves collaborative research, biomarker identification, and advancing translational efforts. Cofilin emerges as a pivotal player, offering potential as a therapeutic target. However, unraveling its complexities requires concerted multidisciplinary efforts for nuanced and effective interventions across the intricate landscape of neurodegenerative diseases and stroke, presenting a hopeful avenue for improved patient care.
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Affiliation(s)
- Faheem Shehjar
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
| | - Daniyah A. Almarghalani
- Stroke Research Unit, Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Reetika Mahajan
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
| | - Syed A.-M. Hasan
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA;
| | - Zahoor A. Shah
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA;
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23
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Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci 2023; 14:13159-13175. [PMID: 38023523 PMCID: PMC10664576 DOI: 10.1039/d3sc04195f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Rommie Elizabeth Amaro
- Department of Molecular Biology, University of California San Diego La Jolla California 92093 USA
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24
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Miura K, Fujihara M, Watanabe M, Takamura Y, Kawasaki M, Nakano S, Kakuta H. Direct evaluation of polarity of the ligand binding pocket in retinoid X receptor using a fluorescent solvatochromic agonist. Bioorg Med Chem Lett 2023; 96:129536. [PMID: 37913851 DOI: 10.1016/j.bmcl.2023.129536] [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: 06/04/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
High selectivity of small-molecule drug candidates for their target molecule is important to minimize potential side effects. One factor that contributes to the selectivity is the internal polarity of the ligand-binding pocket (LBP) in the target molecule, but this is difficult to measure. Here, we first confirmed that the retinoid X receptor (RXR) agonist 6-(ethyl(1-isobutyl-2-oxo-4-(trifluoromethyl)-1,2-dihydroquinolin-7-yl)amino)nicotinic acid (NEt-iFQ, 1) exhibits fluorescence solvatochromism, i.e., its Stokes shift depends on the polarity of the solvent, and then we utilized this property to directly measure the internal polarity of the RXRα-LBP. The Stokes shift of 1 when bound to the RXRα-LBP corresponded to that of 1 in chloroform solution. This finding is expected to be helpful for designing RXR-selective ligands. A similar approach should be appliable to evaluate the internal polarity of the LBPs of other receptors.
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Affiliation(s)
- Kizuku Miura
- Faculty of Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan; Department of Liberal Arts, The Open University of Japan, 2-11 Wakaba, Mihama-ku, Chiba 261- 8586, Japan
| | - Masaki Watanabe
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Yuta Takamura
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Mayu Kawasaki
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52- 1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52- 1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan.
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25
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Puszko AK, Sosnowski P, Hermine O, Hopfgartner G, Lepelletier Y, Misicka A. Structure-activity relationship studies and biological properties evaluation of peptidic NRP-1 ligands: Investigation of N-terminal cysteine importance. Bioorg Med Chem 2023; 94:117482. [PMID: 37774449 DOI: 10.1016/j.bmc.2023.117482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Neuropilin-1 (NRP-1) is a major co-receptor of vascular endothelial growth factor receptor-2 (VEGFR-2). It may also stimulate tumour growth and metastasis independently of VEGF-A165. These functions make VEGF-A165/NRP-1 complex formation and its inhibition of great interest, where NRP-1 is the target for which effective ligands are sought. Design of peptide-like inhibitors represent a strategy with great potential in the treatment of NRP-1-related disorders. Here, we present the synthesis, molecular modelling, structure-activity relationship studies as well as biological evaluation of peptides with the branched sequences H2N-X-Lys(hArg)-Dab-Oic-Arg-OH and H2N-Lys(X-hArg)-Dab-Oic-Arg-OH. Two of the designed peptides, in which Cys was inserted in X position, expressed high affinity (∼40 nM value) for NRP-1 and were resistant to enzymatic digestion in human serum. Moreover, peptide/NRP-1 complex promoted fast intracytoplasmic protein trafficking towards the plasma membrane in breast cancer cells. Our results suggest that these compounds might be good candidates for further development of VEGF-A165/NRP-1 inhibitors.
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Affiliation(s)
- Anna K Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Piotr Sosnowski
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland; Department of Bioanalytics, Medical University of Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Olivier Hermine
- Université Paris Cité, Imagine Institute, 24 boulevard Montparnasse, 75015 Paris, France; INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
| | - Gérard Hopfgartner
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Yves Lepelletier
- Université Paris Cité, Imagine Institute, 24 boulevard Montparnasse, 75015 Paris, France; INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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26
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Fenwick M, Reers AR, Liu Y, Zigweid R, Sankaran B, Shin J, Hulverson MA, Hammerson B, Fernández Álvaro E, Myler PJ, Kaushansky A, Van Voorhis WC, Fan E, Staker BL. Identification of and Structural Insights into Hit Compounds Targeting N-Myristoyltransferase for Cryptosporidium Drug Development. ACS Infect Dis 2023; 9:1821-1833. [PMID: 37722671 PMCID: PMC10580320 DOI: 10.1021/acsinfecdis.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 09/20/2023]
Abstract
Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.
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Affiliation(s)
- Michael
K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Alexandra R. Reers
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Yi Liu
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Advanced Light Source, Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Janis Shin
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Bradley Hammerson
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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27
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Pratap Reddy Gajulapalli V. Development of Kinase-Centric Drugs: A Computational Perspective. ChemMedChem 2023; 18:e202200693. [PMID: 37442809 DOI: 10.1002/cmdc.202200693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
Kinases are prominent drug targets in the pharmaceutical and research community due to their involvement in signal transduction, physiological responses, and upon dysregulation, in diseases such as cancer, neurological and autoimmune disorders. Several FDA-approved small-molecule drugs have been developed to combat human diseases since Gleevec was approved for the treatment of chronic myelogenous leukemia. Kinases were considered "undruggable" in the beginning. Several FDA-approved small-molecule drugs have become available in recent years. Most of these drugs target ATP-binding sites, but a few target allosteric sites. Among kinases that belong to the same family, the catalytic domain shows high structural and sequence conservation. Inhibitors of ATP-binding sites can cause off-target binding. Because members of the same family have similar sequences and structural patterns, often complex relationships between kinases and inhibitors are observed. To design and develop drugs with desired selectivity, it is essential to understand the target selectivity for kinase inhibitors. To create new inhibitors with the desired selectivity, several experimental methods have been designed to profile the kinase selectivity of small molecules. Experimental approaches are often expensive, laborious, time-consuming, and limited by the available kinases. Researchers have used computational methodologies to address these limitations in the design and development of effective therapeutics. Many computational methods have been developed over the last few decades, either to complement experimental findings or to forecast kinase inhibitor activity and selectivity. The purpose of this review is to provide insight into recent advances in theoretical/computational approaches for the design of new kinase inhibitors with the desired selectivity and optimization of existing inhibitors.
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28
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Yoon HJ, Kundu S, Wu S. Molecular Dynamics Simulation Study of the Selective Inhibition of Coagulation Factor IXa over Factor Xa. Molecules 2023; 28:6909. [PMID: 37836752 PMCID: PMC10574344 DOI: 10.3390/molecules28196909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Thromboembolic disorders, arising from abnormal coagulation, pose a significant risk to human life in the modern world. The FDA has recently approved several anticoagulant drugs targeting factor Xa (FXa) to manage these disorders. However, these drugs have potential side effects, leading to bleeding complications in patients. To mitigate these risks, coagulation factor IXa (FIXa) has emerged as a promising target due to its selective regulation of the intrinsic pathway. Due to the high structural and functional similarities of these coagulation factors and their inhibitor binding modes, designing a selective inhibitor specifically targeting FIXa remains a challenging task. The dynamic behavior of protein-ligand interactions and their impact on selectivity were analyzed using molecular dynamics simulation, considering the availability of potent and selective compounds for both coagulation factors and the co-crystal structures of protein-ligand complexes. Throughout the simulations, we examined ligand movements in the binding site, as well as the contact frequencies and interaction fingerprints, to gain insights into selectivity. Interaction fingerprint (IFP) analysis clearly highlights the crucial role of strong H-bond formation between the ligand and D189 and A190 in the S1 subsite for FIXa selectivity, consistent with our previous study. This dynamic analysis also reveals additional FIXa-specific interactions. Additionally, the absence of polar interactions contributes to the selectivity for FXa, as observed from the dynamic profile of interactions. A contact frequency analysis of the protein-ligand complexes provides further confirmation of the selectivity criteria for FIXa and FXa, as well as criteria for binding and activity. Moreover, a ligand movement analysis reveals key interaction dynamics that highlight the tighter binding of selective ligands to the proteins compared to non-selective and inactive ligands.
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Affiliation(s)
- Hyun Jung Yoon
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea;
| | - Sibsankar Kundu
- R&D Center, PharmCADD Co., Ltd., Busan 48792, Republic of Korea;
| | - Sangwook Wu
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea;
- R&D Center, PharmCADD Co., Ltd., Busan 48792, Republic of Korea;
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29
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Dwivedi S, Chavan A, Paul AT. SET7, a lysine-specific methyl transferase: An intriguing epigenetic target to combat diabetic nephropathy. Drug Discov Today 2023; 28:103754. [PMID: 37648018 DOI: 10.1016/j.drudis.2023.103754] [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: 04/24/2023] [Revised: 07/14/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
Diabetic nephropathy (DN) is a dreadful complication of diabetes that affects ∼50% of diabetics and is a leading cause of end-stage renal disease (ESRD). Studies have linked aberrant expression of lysine methyltransferases (KMTs) to the onset and progression of DN. SET7 is a KMT that methylates specific lysine residues of the histone and nonhistone proteins. It plays an important role in the transforming growth factor-β (TGF-β)-induced upregulation of extracellular matrix (ECM)-associated genes that are responsible for the inflammatory cascade observed in DN. Inhibiting SET7 has potential to attenuate renal disorders in animal studies. This review will focus on the role of SET7 in DN and its potential as a therapeutic target to combat DN.
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Affiliation(s)
- Samarth Dwivedi
- Natural Product Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science (Pilani Campus), Pilani 333031, Rajasthan, India
| | - Atharva Chavan
- Natural Product Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science (Pilani Campus), Pilani 333031, Rajasthan, India
| | - Atish T Paul
- Natural Product Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science (Pilani Campus), Pilani 333031, Rajasthan, India.
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30
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Oehler S, Lucaroni L, Migliorini F, Elsayed A, Prati L, Puglioli S, Matasci M, Schira K, Scheuermann J, Yudin D, Jia M, Ban N, Bushnell D, Kornberg R, Cazzamalli S, Neri D, Favalli N, Bassi G. A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition. Nat Chem 2023; 15:1431-1443. [PMID: 37400597 DOI: 10.1038/s41557-023-01257-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.
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Affiliation(s)
| | | | | | - Abdullah Elsayed
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Kristina Schira
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Denis Yudin
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Min Jia
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | - Roger Kornberg
- NeoTX Therapeutics LTD, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | - Dario Neri
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Philogen SPA, Siena, Italy
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Naomi R, Teoh SH, Embong H, Balan SS, Othman F, Mamat-Hamidi K, Bahari H, Yazid MD. Analyzing Active Compounds in Elateriospermum tapos Yogurt for Maternal Obesity: A Network Pharmacology and Molecular Docking Study. Foods 2023; 12:3575. [PMID: 37835227 PMCID: PMC10572448 DOI: 10.3390/foods12193575] [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: 09/02/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Maternal obesity, characterized by an elevated body mass index (BMI) during pregnancy, is known to have adverse effects on the offspring. However, a recent study suggests that Elateriospermum tapos (E. tapos) yogurt may hold potential in mitigating excessive weight retention post-pregnancy. Thus, this study aims to employ network pharmacology to explore the pharmacological effects of the bioactive compounds present in E. tapos yogurt against maternal obesity. Initially, a screening process is conducted to identify the bioactive compounds in E. tapos yogurt, followed by the prediction of potential gene targets for these compounds using Swiss Target Prediction and the SuperPred databases. Maternal obesity-associated genes are sourced from the OMIM, DisGeNet, and GeneCards databases. The interaction between the identified compounds and maternal obesity genes is established via protein-protein interaction analysis, gene ontology examination, and KEGG pathway analysis. To validate the results, molecular docking studies are conducted using AutoDock Tools software. The findings reveal that out of the 64 compounds analyzed, three meet the screening criteria, resulting in a total of 380 potential gene targets. Among these targets, 240 are shared with maternal obesity-related genes. Further analysis demonstrates the favorable affinity of these active compounds with key targets, linking them to biological processes involving protein phosphorylation, inflammation, as well as the pathways related to lipid metabolism, atherosclerosis, and the other signaling pathways. In conclusion, this study provides valuable insights into the potential pharmacological effects of the bioactive compounds found in E. tapos yogurt against maternal obesity. These findings open avenues for further exploration and potential therapeutic interventions targeting maternal obesity.
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Affiliation(s)
- Ruth Naomi
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Soo Huat Teoh
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang 13200, Malaysia;
| | - Hashim Embong
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
| | - Santhra Segaran Balan
- Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Shah Alam 40100, Malaysia;
| | - Fezah Othman
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Kamalludin Mamat-Hamidi
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Selangor 43400, Malaysia;
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Hasnah Bahari
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Muhammad Dain Yazid
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
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32
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Li Q, Deng X, Xu YJ, Dong L. Development of Long-Acting Dipeptidyl Peptidase-4 Inhibitors: Structural Evolution and Long-Acting Determinants. J Med Chem 2023; 66:11593-11631. [PMID: 37647598 DOI: 10.1021/acs.jmedchem.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Considerable effort has been made to achieve less frequent dosing in the development of DPP-4 inhibitors. Enthusiasm for long-acting DPP-4 inhibitors is based on the promise that such agents with less frequent dosing regimens are associated with improved patient adherence, but the rational design of long-acting DPP-4 inhibitors remains a major challenge. In this Perspective, the development of long-acting DPP-4 inhibitors is comprehensively summarized to highlight the evolution of initial lead compounds on the path toward developing long-acting DPP-4 inhibitors over nearly three decades. The determinants for long duration of action are then examined, including the nature of the target, potency, binding kinetics, crystal structures, selectivity, and preclinical and clinical pharmacokinetic and pharmacodynamic profiles. More importantly, several possible approaches for the rational design of long-acting drugs are discussed. We hope that this information will facilitate the design and development of safer and more effective long-acting DPP-4 inhibitors and other oral drugs.
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Affiliation(s)
- Qing Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Xiaoyan Deng
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Yan-Jun Xu
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Lin Dong
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Boopathi V, Nahar J, Murugesan M, Subramaniyam S, Kong BM, Choi SK, Lee CS, Ling L, Yang DU, Yang DC, Mathiyalagan R, Chan Kang S. In silico and in vitro inhibition of host-based viral entry targets and cytokine storm in COVID-19 by ginsenoside compound K. Heliyon 2023; 9:e19341. [PMID: 37809955 PMCID: PMC10558348 DOI: 10.1016/j.heliyon.2023.e19341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that emerged as an epidemic, causing a respiratory disease with multiple severe symptoms and deadly consequences. ACE-2 and TMPRSS2 play crucial and synergistic roles in the membrane fusion and viral entry of SARS-CoV-2 (COVID-19). The spike (S) protein of SARS-CoV-2 binds to the ACE-2 receptor for viral entry, while TMPRSS2 proteolytically cleaves the S protein into S1 and S2 subunits, promoting membrane fusion. Therefore, ACE-2 and TMPRSS2 are potential drug targets for treating COVID-19, and their inhibition is a promising strategy for treatment and prevention. This study proposes that ginsenoside compound K (G-CK), a triterpenoid saponin abundant in Panax Ginseng, a dietary and medicinal herb highly consumed in Korea and China, effectively binds to and inhibits ACE-2 and TMPRSS2 expression. We initially conducted an in-silico evaluation where G-CK showed a high affinity for the binding sites of the two target proteins of SARS-CoV-2. Additionally, we evaluated the stability of G-CK using molecular dynamics (MD) simulations for 100 ns, followed by MM-PBSA calculations. The MD simulations and free energy calculations revealed that G-CK has stable and favorable energies, leading to strong binding with the targets. Furthermore, G-CK suppressed ACE2 and TMPRSS2 mRNA expression in A549, Caco-2, and MCF7 cells at a concentration of 12.5 μg/mL and in LPS-induced RAW 264.7 cells at a concentration of 6.5 μg/mL, without significant cytotoxicity.ACE2 and TMPRSS2 expression were significantly lower in A549 and RAW 264.7 cells following G-CK treatment. These findings suggest that G-CK may evolve as a promising therapeutic against COVID-19.
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Affiliation(s)
- Vinothini Boopathi
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Jinnatun Nahar
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Mohanapriya Murugesan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | | | - Byoung Man Kong
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Sung-Keun Choi
- Daedong Korea Ginseng Co., Ltd, 86, Gunbuk-ro, Gunbuk-myeon, Geumsan-gun, Chungcheongnam-do 32718 Republic of Korea
| | - Chang-Soon Lee
- Daedong Korea Ginseng Co., Ltd, 86, Gunbuk-ro, Gunbuk-myeon, Geumsan-gun, Chungcheongnam-do 32718 Republic of Korea
| | - Li Ling
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Dong Uk Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Se Chan Kang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
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Singh H, Almaazmi SY, Dutta T, Keyzers RA, Blatch GL. In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria. Front Mol Biosci 2023; 10:1158912. [PMID: 37621993 PMCID: PMC10445141 DOI: 10.3389/fmolb.2023.1158912] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Plasmodium falciparum is a unicellular, intracellular protozoan parasite, and the causative agent of malaria in humans, a deadly vector borne infectious disease. A key phase of malaria pathology, is the invasion of human erythrocytes, resulting in drastic remodeling by exported parasite proteins, including molecular chaperones and co-chaperones. The survival of the parasite within the human host is mediated by P. falciparum heat shock protein 70s (PfHsp70s) and J domain proteins (PfJDPs), functioning as chaperones-co-chaperones partnerships. Two complexes have been shown to be important for survival and pathology of the malaria parasite: PfHsp70-x-PFE0055c (exported); and PfHsp70-2-PfSec63 (endoplasmic reticulum). Virtual screening was conducted on the drug repurposing library, the Pandemic Response Box, to identify small-molecules that could specifically disrupt these chaperone complexes. Five top ranked compounds possessing preferential binding affinity for the malarial chaperone system compared to the human system, were identified; three top PfHsp70-PfJDP binders, MBX 1641, zoliflodacin and itraconazole; and two top J domain binders, ezetimibe and a benzo-diazepinone. These compounds were validated by repeat molecular dockings and molecular dynamics simulation, resulting in all the compounds, except for MBX 1461, being confirmed to bind preferentially to the malarial chaperone system. A detailed contact analysis of the PfHsp70-PfJDP binders identified two different types of modulators, those that potentially inhibit complex formation (MBX 1461), and those that potentially stabilize the complex (zoliflodacin and itraconazole). These data suggested that zoliflodacin and itraconazole are potential novel modulators specific to the malarial system. A detailed contact analysis of the J domain binders (ezetimibe and the benzo-diazepinone), revealed that they bound with not only greater affinity but also a better pose to the malarial J domain compared to that of the human system. These data suggested that ezetimibe and the benzo-diazepinone are potential specific inhibitors of the malarial chaperone system. Both itraconazole and ezetimibe are FDA-approved drugs, possess anti-malarial activity and have recently been repurposed for the treatment of cancer. This is the first time that such drug-like compounds have been identified as potential modulators of PfHsp70-PfJDP complexes, and they represent novel candidates for validation and development into anti-malarial drugs.
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Affiliation(s)
- Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Shaikha Y. Almaazmi
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Tanima Dutta
- Department of Diagnostic Genomics, Path West Nedlands, QEII Medical Centre, Nedlands, WA, Australia
| | - Robert A. Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L. Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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35
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Ya'ar Bar S, Pintel N, Abd Alghne H, Khattib H, Avni D. The therapeutic potential of sphingolipids for cardiovascular diseases. Front Cardiovasc Med 2023; 10:1224743. [PMID: 37608809 PMCID: PMC10440740 DOI: 10.3389/fcvm.2023.1224743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/24/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide and Inflammation plays a critical role in the development of CVD. Despite considerable progress in understanding the underlying mechanisms and various treatment options available, significant gaps in therapy necessitate the identification of novel therapeutic targets. Sphingolipids are a family of lipids that have gained attention in recent years as important players in CVDs and the inflammatory processes that underlie their development. As preclinical studies have shown that targeting sphingolipids can modulate inflammation and ameliorate CVDs, targeting sphingolipids has emerged as a promising therapeutic strategy. This review discusses the current understanding of sphingolipids' involvement in inflammation and cardiovascular diseases, the existing therapeutic approaches and gaps in therapy, and explores the potential of sphingolipids-based drugs as a future avenue for CVD treatment.
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Affiliation(s)
- Sapir Ya'ar Bar
- Department of Natural Compound, Nutrition, and Health, MIGAL, Kiryat Shmona, Israel
| | - Noam Pintel
- Department of Natural Compound, Nutrition, and Health, MIGAL, Kiryat Shmona, Israel
| | - Hesen Abd Alghne
- Department of Natural Compound, Nutrition, and Health, MIGAL, Kiryat Shmona, Israel
- Tel-Hai College Department of Biotechnology, Kiryat Shmona, Israel
| | - Hamdan Khattib
- Department of Natural Compound, Nutrition, and Health, MIGAL, Kiryat Shmona, Israel
- Department of Gastroenterology and Hepatology, Tel Aviv University Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Dorit Avni
- Department of Natural Compound, Nutrition, and Health, MIGAL, Kiryat Shmona, Israel
- Tel-Hai College Department of Biotechnology, Kiryat Shmona, Israel
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36
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Huth SW, Oakley JV, Seath CP, Geri JB, Trowbridge AD, Parker DL, Rodriguez-Rivera FP, Schwaid AG, Ramil C, Ryu KA, White CH, Fadeyi OO, Oslund RC, MacMillan DWC. μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping. J Am Chem Soc 2023; 145:16289-16296. [PMID: 37471577 PMCID: PMC10809032 DOI: 10.1021/jacs.3c03325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discovery, but in many cases structural characterization is challenging or impossible. PAL has also enabled binding site mapping with peptide- and amino-acid-level resolution; however, the stoichiometric activation mode can lead to poor signal and coverage of the resident binding pocket. Additionally, each PAL probe can have its own fragmentation pattern, complicating the analysis by mass spectrometry. Here, we establish a robust and general photocatalytic approach toward the mapping of protein binding sites, which we define as identification of residues proximal to the ligand binding pocket. By utilizing a catalytic mode of activation, we obtain sets of labeled amino acids in the proximity of the target protein binding site. We use this methodology to map, in vitro, the binding sites of six protein targets, including several kinases and molecular glue targets, and furthermore to investigate the binding site of the STAT3 inhibitor MM-206, a ligand with no known crystal structure. Finally, we demonstrate the successful mapping of drug binding sites in live cells. These results establish μMap as a powerful method for the generation of amino-acid- and peptide-level target engagement data.
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Affiliation(s)
- Sean W. Huth
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - James V. Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jacob B. Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Aaron D. Trowbridge
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Adam G. Schwaid
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Carlo Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Cory H. White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Olugbeminiyi O. Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Rob C. Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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37
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Rauthe P, Sabljo K, Vogelbacher MK, Feldmann C, Unterreiner AN. Excited State Dynamics of Alizarin Red S Nanoparticles in Solution. Molecules 2023; 28:5633. [PMID: 37570603 PMCID: PMC10420268 DOI: 10.3390/molecules28155633] [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: 07/03/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Alizarin red S is a sulfonated, water-soluble derivative of alizarin. This work presents femtosecond studies of alizarin red S (ARS) nanoparticles in comparison to ARS in aqueous solution and to alizarin in DMSO. The femtosecond studies cover a probing spectral range of 350-750 nm using different excitation wavelengths, taking into account the variation of the absorption spectra with the pH values of the solvent. Stationary absorption spectra show slight differences between solution and nanoparticles. Excitation at 530 nm results in low and noisy responses, therefore, we additionally recorded transient spectra of the nanoparticles at λex = 267 nm. While the results in DMSO are comparable to previous studies in non-aqueous solvents, we report a relatively fast relaxation of 14 ps in [La(OH)2][ARS] nanoparticles in aqueous solution after excitation at 530 nm, which is similar to Na(ARS) solution (19 ps). The dynamics changed with lower pH, but still without significant differences between nanoparticles and solution. We propose [La(OH)2][ARS] nanoparticles as a suitable alternative to dissolved molecules with similar spectroscopic properties, for example, with regard to biomarker applications.
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Affiliation(s)
- Pascal Rauthe
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Kristina Sabljo
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | | | - Claus Feldmann
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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38
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Powers AS, Pham V, Burger WAC, Thompson G, Laloudakis Y, Barnes NW, Sexton PM, Paul SM, Christopoulos A, Thal DM, Felder CC, Valant C, Dror RO. Structural basis of efficacy-driven ligand selectivity at GPCRs. Nat Chem Biol 2023; 19:805-814. [PMID: 36782010 PMCID: PMC10299909 DOI: 10.1038/s41589-022-01247-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 02/15/2023]
Abstract
A drug's selectivity for target receptors is essential to its therapeutic utility, but achieving selectivity between similar receptors is challenging. The serendipitous discovery of ligands that stimulate target receptors more strongly than closely related receptors, despite binding with similar affinities, suggests a solution. The molecular mechanism of such 'efficacy-driven selectivity' has remained unclear, however, hindering design of such ligands. Here, using atomic-level simulations, we reveal the structural basis for the efficacy-driven selectivity of a long-studied clinical drug candidate, xanomeline, between closely related muscarinic acetylcholine receptors (mAChRs). Xanomeline's binding mode is similar across mAChRs in their inactive states but differs between mAChRs in their active states, with divergent effects on active-state stability. We validate this mechanism experimentally and use it to design ligands with altered efficacy-driven selectivity. Our results suggest strategies for the rational design of ligands that achieve efficacy-driven selectivity for many pharmaceutically important G-protein-coupled receptors.
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Affiliation(s)
- Alexander S Powers
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Yianni Laloudakis
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Nicholas W Barnes
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | | | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Neuromedicines Discovery Center, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | | | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
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39
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Koroleva EV, Kornoushenko YV, Karpenko AD, Bosko IP, Siniutsich JV, Ignatovich ZV, Andrianov AM. In silico design and computational evaluation of novel 2-arylaminopyrimidine-based compounds as potential multi-targeted protein kinase inhibitors: application for the native and mutant (T315I) Bcr-Abl tyrosine kinase. J Biomol Struct Dyn 2023; 41:4065-4080. [PMID: 35470777 DOI: 10.1080/07391102.2022.2062784] [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: 06/15/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
An integrated computational approach to drug discovery was used to identify novel potential inhibitors of the native and mutant (T315I) Bcr-Abl tyrosine kinase, the enzyme playing a key role in the pathogenesis of chronic myeloid leukemia (CML). This approach included i) design of chimeric molecules based on the 2-arylaminopyrimidine fragment, the main pharmacophore of the Abl kinase inhibitors imatinib and nilotinib used in the clinic for the CML treatment, ii) molecular docking of these compounds with the ATP-binding site of the native and mutant Abl kinase, iii) refinement of the ligand-binding poses by the quantum chemical method PM7, iv) molecular dynamics simulations of the ligand/Abl complexes, and v) prediction of the ligand/Abl binding affinity in terms of scoring functions of molecular docking, machine learning, quantum chemistry, and molecular dynamics. As a result, five top-ranking compounds able to effectively block the enzyme catalytic site were identified. According to the data obtained, these compounds exhibit close modes of binding to the Abl kinase active site that are mainly provided by hydrogen bonds and multiple van der Waals contacts. The identified compounds show high binding affinity to the native and mutant Abl kinase comparable with the one calculated for the FDA-approved kinase-targeted inhibitors imatinib, nilotinib, and ponatinib used in the calculations as a positive control. The results obtained testify to the predicted drug candidates against CML may serve as good scaffolds for the design of novel anticancer agents able to target the ATP-binding pocket of the native and mutant Abl kinase.Communicated by Ramaswamy H. Sarma.
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MESH Headings
- Humans
- Adenosine Triphosphate/metabolism
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Catalytic Domain
- Computer Simulation
- Drug Design
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Hydrogen Bonding
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Ligands
- Machine Learning
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Mutant Proteins/antagonists & inhibitors
- Mutant Proteins/genetics
- Mutation
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
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Affiliation(s)
- Elena V Koroleva
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Anna D Karpenko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Ivan P Bosko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Julia V Siniutsich
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Zhanna V Ignatovich
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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40
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Soleymani T, Chen TY, Gonzalez-Kozlova E, Dogra N. The human neurosecretome: extracellular vesicles and particles (EVPs) of the brain for intercellular communication, therapy, and liquid-biopsy applications. Front Mol Biosci 2023; 10:1156821. [PMID: 37266331 PMCID: PMC10229797 DOI: 10.3389/fmolb.2023.1156821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Emerging evidence suggests that brain derived extracellular vesicles (EVs) and particles (EPs) can cross blood-brain barrier and mediate communication among neurons, astrocytes, microglial, and other cells of the central nervous system (CNS). Yet, a complete understanding of the molecular landscape and function of circulating EVs & EPs (EVPs) remain a major gap in knowledge. This is mainly due to the lack of technologies to isolate and separate all EVPs of heterogeneous dimensions and low buoyant density. In this review, we aim to provide a comprehensive understanding of the neurosecretome, including the extracellular vesicles that carry the molecular signature of the brain in both its microenvironment and the systemic circulation. We discuss the biogenesis of EVPs, their function, cell-to-cell communication, past and emerging isolation technologies, therapeutics, and liquid-biopsy applications. It is important to highlight that the landscape of EVPs is in a constant state of evolution; hence, we not only discuss the past literature and current landscape of the EVPs, but we also speculate as to how novel EVPs may contribute to the etiology of addiction, depression, psychiatric, neurodegenerative diseases, and aid in the real time monitoring of the "living brain". Overall, the neurosecretome is a concept we introduce here to embody the compendium of circulating particles of the brain for their function and disease pathogenesis. Finally, for the purpose of inclusion of all extracellular particles, we have used the term EVPs as defined by the International Society of Extracellular Vesicles (ISEV).
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Affiliation(s)
- Taliah Soleymani
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tzu-Yi Chen
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Edgar Gonzalez-Kozlova
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Navneet Dogra
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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41
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Emmerich TD, Hayes JM. In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development. Pharmaceuticals (Basel) 2023; 16:ph16050661. [PMID: 37242443 DOI: 10.3390/ph16050661] [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: 04/02/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) isoforms α and β have diverse roles within cell biology, and have been linked with multiple diseases that include prominent CNS conditions such as Alzheimer's disease and several psychiatric disorders. In this study, motivated by computation, we aimed to identify novel ATP-binding site inhibitors of GSK-3 with CNS-active potential. A ligand screening (docking) protocol against GSK-3β was first optimized, employing an active/decoy benchmarking set, with the final protocol selected based on statistical performance analysis. The optimized protocol involved pre-filtering of ligands using a three-point 3D-pharmacophore, followed by Glide-SP docking applying hinge region hydrogen bonding constraints. Using this approach, the Biogenic subset of the ZINC15 compound database was screened, focused on compounds with potential for CNS-activity. Twelve compounds (generation I) were selected for experimental validation using in vitro GSK-3β binding assays. Two hit compounds, 1 and 2, with 6-amino-7H-benzo[e]perimidin-7-one and 1-(phenylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione type scaffolds were identified with IC50 values of 1.63 µM and 20.55 µM, respectively. Ten analogues of 2 (generation II) were selected for structure activity relationship (SAR) analysis and revealed four low micromolar inhibitors (<10 µM), with 19 (IC50 = 4.1 µM)~five times more potent than initial hit compound 2. Selectivity screening of low micromolar inhibitors 14 and 19 (comparing aryl- and alkyl-substituents) against 10 homologous kinases revealed unique selectivity profiles, with both compounds more potent against the GSK-3α isoform (IC50s~2 µM) and, additionally, inhibitors of PKBβ (IC50s < 25 µM). Compound 14 also inhibited ERK2 and 19, PKCγ, but generally good selectivity for GSK-3 isoforms over the other kinases was observed. The compounds had excellent predicted oral bioavailability and CNS-activity profiles, presenting promising candidates for future testing in cellular models of disease.
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Affiliation(s)
- Thomas D Emmerich
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Joseph M Hayes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
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42
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Khayat MT, Ahmed HEA, Omar AM, Muhammad YA, Mohammad KA, Malebari AM, Khayyat AN, Halawa AH, Abulkhair HS, Al-Karmalawy AA, Almaghrabi M, Alharbi M, Aljahdali AS, El-Agrody AM. A novel class of phenylpyrazolone-sulphonamides rigid synthetic anticancer molecules selectively inhibit the isoform IX of carbonic anhydrases guided by molecular docking and orbital analyses. J Biomol Struct Dyn 2023; 41:15243-15261. [PMID: 36914238 DOI: 10.1080/07391102.2023.2188957] [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: 01/02/2023] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
All the previously reported phenylpyrazoles as carbonic anhydrase inhibitors (CAIs) were found to have small sizes and high levels of flexibility, and hence showed low selectivity profiles toward a particular isoform of CA. Herein, we report the development of a more rigid ring system bearing a sulfonamide hydrophilic head and a lipophilic tail to develop novel molecules that are suggested to have a better selectivity toward a special CA isoform. Accordingly, three novel sets of pyrano[2,3-c]pyrazoles attached with sulfonamide head and aryl hydrophobic tail were synthesized to enhance the selectivity toward a specific isoform of human carbonic anhydrases (hCAs). The impact of both attachments on the potency and selectivity has been extensively discussed in terms of in vitro cytotoxicity evaluation under hypoxic conditions, structure-activity relationship and carbonic anhydrase enzyme assay. All of the new candidates displayed good cytotoxic activities against breast and colorectal carcinomas. Results of the carbonic anhydrase enzyme assay demonstrated the preferential of compounds 22, 24 and 27 to inhibit the isoform IX of hCAs selectively. Wound-healing assay has also been performed and revealed the potential of 27 to decrease the wound closure percentage in MCF-7 cells. Molecular docking and molecular orbital analysis have finally been conducted. Results indicate the potential binding interactions of 24 and 27 with several crucial amino acids of the hCA IX.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maan T Khayat
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hany E A Ahmed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Nasr City, Egypt
| | - Abdelsattar M Omar
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Nasr City, Egypt
| | - Yosra A Muhammad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khadijah A Mohammad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Azizah M Malebari
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahdab N Khayyat
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed H Halawa
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Nasr City, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Majed Alharbi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anfal S Aljahdali
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
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43
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A review on cyclin-dependent kinase 5: An emerging drug target for neurodegenerative diseases. Int J Biol Macromol 2023; 230:123259. [PMID: 36641018 DOI: 10.1016/j.ijbiomac.2023.123259] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Cyclin-dependent kinase 5 (CDK5) is the serine/threonine-directed kinase mainly found in the brain and plays a significant role in developing the central nervous system. Recent evidence suggests that CDK5 is activated by specific cyclins regulating its expression and activity. P35 and p39 activate CDK5, and their proteolytic degradation produces p25 and p29, which are stable products involved in the hyperphosphorylation of tau protein, a significant hallmark of various neurological diseases. Numerous high-affinity inhibitors of CDK5 have been designed, and some are marketed drugs. Roscovitine, like other drugs, is being used to minimize neurological symptoms. Here, we performed an extensive literature analysis to highlight the role of CDK5 in neurons, synaptic plasticity, DNA damage repair, cell cycle, etc. We have investigated the structural features of CDK5, and their binding mode with the designed inhibitors is discussed in detail to develop attractive strategies in the therapeutic targeting of CDK5 for neurodegenerative diseases. This review provides deeper mechanistic insights into the therapeutic potential of CDK5 inhibitors and their implications in the clinical management of neurodegenerative diseases.
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44
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Szabó L, Tanguturi P, Goodman HJ, Sprőber S, Liu C, Al-Obeidi F, Bartlett MJ, Falk T, Kumirov VK, Heien ML, Streicher JM, Polt R. Structure-Based Design of Glycosylated Oxytocin Analogues with Improved Selectivity and Antinociceptive Activity. ACS Med Chem Lett 2023; 14:163-170. [PMID: 36793431 PMCID: PMC9923833 DOI: 10.1021/acsmedchemlett.2c00455] [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: 10/24/2022] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Acute and chronic pain is often treated with opioids despite the negative side effects of constipation, physical dependence, respiratory depression, and overdose. The misuse of opioid analgesics has given rise to the opioid crisis/epidemic, and alternate nonaddictive analgesics are urgently needed. Oxytocin, a pituitary hormone, is an alternative to the small molecule treatments available and has been used as an analgesic as well as for the treatment and prevention of opioid use disorder (OUD). Clinical implementation is limited by its poor pharmacokinetic profile, a result of the labile disulfide bond between two cysteine residues in the native sequence. Stable brain penetrant oxytocin analogues have been synthesized by replacement of the disulfide bond with a stable lactam and glycosidation of the C-terminus. These analogues show exquisite selectivity for the oxytocin receptor and potent in vivo antinociception in mice following peripheral (i.v.) administration, supporting further study of their clinical potential.
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Affiliation(s)
- Lajos
Z. Szabó
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
| | | | - Hannah J. Goodman
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
| | - Sára Sprőber
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
- Visiting
Student, Budapest University of Technology
and Economics, 1111Budapest, Műegyetem
rkp. 3, Hungary
| | - Chenxi Liu
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
| | - Fahad Al-Obeidi
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
| | - Mitchell J. Bartlett
- Department
of Neurology, College of Medicine, The University
of Arizona, Tucson, Arizona85724, United
States
| | - Torsten Falk
- Department
of Pharmacology, College of Medicine, The
University of Arizona, Tucson, Arizona85724, United States
- Department
of Neurology, College of Medicine, The University
of Arizona, Tucson, Arizona85724, United
States
| | - Vlad K. Kumirov
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
| | - M. Leandro Heien
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
- Comprehensive
Pain and Addiction Center, The University
of Arizona, Tucson, Arizona85724, United States
| | - John M. Streicher
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
- Comprehensive
Pain and Addiction Center, The University
of Arizona, Tucson, Arizona85724, United States
| | - Robin Polt
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona85721, United States
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45
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Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists. Pharmaceutics 2023; 15:pharmaceutics15020527. [PMID: 36839848 PMCID: PMC9962304 DOI: 10.3390/pharmaceutics15020527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Selective antiadhesion antagonists of Uropathogenic Escherichia coli (UPEC) type-1 Fimbrial adhesin (FimH) are attractive alternatives for antibiotic therapies and prophylaxes against acute or recurrent urinary tract infections (UTIs) caused by UPECs. A rational small library of FimH antagonists based on previously described C-linked allyl α-D-mannopyranoside was synthesized using Heck cross-coupling reaction using a series of iodoaryl derivatives. This work reports two new members of FimH antagonist amongst the above family with sub nanomolar affinity. The resulting hydrophobic aglycones, including constrained alkene and aryl groups, were designed to provide additional favorable binding interactions with the so-called FimH "tyrosine gate". The newly synthesized C-linked glycomimetic antagonists, having a hydrolytically stable anomeric linkage, exhibited improved binding when compared to previously published analogs, as demonstrated by affinity measurement through interactions by FimH lectin. The crystal structure of FimH co-crystallized with one of the nanomolar antagonists revealed the binding mode of this inhibitor into the active site of the tyrosine gate. In addition, selected mannopyranoside constructs neither affected bacterial growth or cell viability nor interfered with antibiotic activity. C-linked mannoside antagonists were effective in decreasing bacterial adhesion to human bladder epithelial cells (HTB-9). Therefore, these molecules constituted additional therapeutic candidates' worth further development in the search for potent anti-adhesive drugs against infections caused by UPEC.
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46
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Singhal A, Singh A, Shrivastava A, Khan R. Epitope imprinted polymeric materials: application in electrochemical detection of disease biomarkers. J Mater Chem B 2023; 11:936-954. [PMID: 36606445 DOI: 10.1039/d2tb02135h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epitope imprinting is a promising method for creating specialized recognition sites that resemble natural biorecognition elements. Epitope-imprinted materials have gained a lot of attention recently in a variety of fields, including bioanalysis, drug delivery, and clinical therapy. The vast applications of epitope imprinted polymers are due to the flexibility in choosing monomers, the simplicity in obtaining templates, specificity toward targets, and resistance to harsh environments along with being cost effective in nature. The "epitope imprinting technique," which uses only a tiny subunit of the target as the template during imprinting, offers a way around various drawbacks inherent to biomacromolecule systems i.e., traditional molecular imprinting techniques with regards to the large size of proteins, such as the size, complexity, accessibility, and conformational flexibility of the template. Electrochemical based sensors are proven to be promising tool for the quick, real-time monitoring of biomarkers. This review unravels epitope imprinting techniques, approaches, and strategies and highlights the applicability of these techniques for the electrochemical quantification of biomarkers for timely disease monitoring. In addition, some challenges are discussed along with future prospective developments.
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Affiliation(s)
- Ayushi Singhal
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Amrita Singh
- Department of Biotechnology, Barkatullah University, Habibganj, Bhopal, Madhya Pradesh 462026, India
| | - Apoorva Shrivastava
- Dr D. Y. Patil Biotechnology and Bioinformatics Institute, Dr D. Y. Patil Vidyapeeth, Sr. No. 87-88, Mumbai-Bangalore Highway, Tathawade, Pune, Maharashtra, 411033, India
| | - Raju Khan
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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47
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Lerma Romero JA, Kolmar H. Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening. Methods Mol Biol 2023; 2681:249-274. [PMID: 37405652 DOI: 10.1007/978-1-0716-3279-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
The binding pocket of some therapeutic targets can acquire multiple conformations that, to some extent, depend on the protein dynamics and the interaction with other molecules. The inability to reach the binding pocket can impose a substantial or even insurmountable barrier for the de novo identification or optimization of small-molecule ligands. Herein, we describe a protocol for the engineering of a target protein and a yeast display FACS sorting strategy to identify protein variants with a stable transient binding pocket with improved binding for a cryptic site-specific ligand. This strategy may facilitate drug discovery using the resulting protein variants with accessible binding pockets for ligand screening.
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Affiliation(s)
- Jorge A Lerma Romero
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany.
- Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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48
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Wong KW, Teh SS, Law KP, Ismail IS, Sato K, Mase N, Mah SH. Synthesis of benzylated amine-substituted xanthone derivatives and their antioxidant and anti-inflammatory activities. Arch Pharm (Weinheim) 2023; 356:e2200418. [PMID: 36285691 DOI: 10.1002/ardp.202200418] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Oxidative stress and its constant companion, inflammation, play a critical part in the pathogenesis of many acute and chronic illnesses. The discovery of new multi-targeted drug candidates with antioxidant and anti-inflammatory properties is deemed necessary. Thus, a series of novel xanthone derivatives with halogenated benzyl (4b-4d, 4f-4h) and methoxylated benzyl groups (4e) attached to the butoxy amine substituent were synthesized in this study. The synthesized xanthone derivatives exhibited stronger antioxidant activity against H2 O2 scavenging than the standard drug, α-tocopherol, but weaker towards DPPH scavenging and ferrous ion chelation. Besides that, 4b-4d, 4f-4h demonstrated good anti-inflammatory activities through NO production inhibition towards lipopolysaccharide (LPS)-induced RAW 264.7 cells and showed 2-4 times stronger effects than the standard drug, diclofenac sodium. Moreover, compound 4b with two brominated benzyl groups attached to the butoxy amine substituent suppressed the production of pro-inflammatory cytokines, TNF-α and IL-1β, significantly. Structure-activity relationship elucidated that the halogenated benzylamine substituent plays an important role in contributing the antioxidant and anti-inflammatory activities of xanthones. In summary, xanthone 4b was identified as a potential lead compound to be further developed into antioxidant and anti-inflammatory drugs. Thus, further studies on the related mechanisms of action of 4b are recommended.
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Affiliation(s)
- Ka Woong Wong
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Soek Sin Teh
- Engineering and Processing Division, Energy and Environment Unit, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kung Pui Law
- School of Pre-University Studies, Taylor's College, Subang Jaya, Selangor, Malaysia
| | - Intan Safinar Ismail
- Natural Medicine and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kohei Sato
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Nobuyuki Mase
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Siau Hui Mah
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia.,Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
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49
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Protein-ligand binding affinity prediction with edge awareness and supervised attention. iScience 2022; 26:105892. [PMID: 36691617 PMCID: PMC9860494 DOI: 10.1016/j.isci.2022.105892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/12/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Accurate prediction of protein-ligand binding affinity is crucial in structure-based drug design but remains some challenges even with recent advances in deep learning: (1) Existing methods neglect the edge information in protein and ligand structure data; (2) current attention mechanisms struggle to capture true binding interactions in the small dataset. Herein, we proposed SEGSA_DTA, a SuperEdge Graph convolution-based and Supervised Attention-based Drug-Target Affinity prediction method, where the super edge graph convolution can comprehensively utilize node and edge information and the multi-supervised attention module can efficiently learn the attention distribution consistent with real protein-ligand interactions. Results on the multiple datasets show that SEGSA_DTA outperforms current state-of-the-art methods. We also applied SEGSA_DTA in repurposing FDA-approved drugs to identify potential coronavirus disease 2019 (COVID-19) treatments. Besides, by using SHapley Additive exPlanations (SHAP), we found that SEGSA_DTA is interpretable and further provides a new quantitative analytical solution for structure-based lead optimization.
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50
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An interpretable machine learning model for selectivity of small molecules against homologous protein family. Future Med Chem 2022; 14:1441-1453. [PMID: 36169035 DOI: 10.4155/fmc-2022-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: In the early stages of drug discovery, various experimental and computational methods are used to measure the specificity of small molecules against a target protein. The selectivity of small molecules remains a challenge leading to off-target side effects. Methods: We have developed a multitask deep learning model for predicting the selectivity on closely related homologs of the target protein. The model has been tested on the Janus-activated kinase and dopamine receptor families of proteins. Results & conclusion: The feature-based representation (extended connectivity fingerprint 4) with Extreme Gradient Boosting performed better when compared with deep neural network models in most of the evaluation metrics. Both the Extreme Gradient Boosting and deep neural network models outperformed the graph-based models. Furthermore, to decipher the model decision on selectivity, the important fragments associated with each homologous protein were identified.
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