1
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Chen X, Varghese S, Zhang Z, Du J, Ruan B, Baell JB, Liu X. Drug discovery and optimization based on the co-crystal structure of natural product with target. Eur J Med Chem 2024; 266:116126. [PMID: 38232464 DOI: 10.1016/j.ejmech.2024.116126] [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: 12/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Due to their structural diversities and prevalent biological activities, natural products (NPs) are momentous resources for drug discovery. Although NPs have a wide range of biological activities, many exhibit structural complexity that leads to synthetic difficulties, which combines with inefficient biological activity, toxicity, and unfavorable pharmacokinetic characteristics and ultimately imparts poor safety and efficacy outcomes. Progress in crystallization and computational techniques allow crystallography to have a seasonable influences on drug discovery. By co-crystallizing with proteins, therapeutic targets of NPs in specific diseases can be identified. By analyzing the co-crystal information, the structure-activity relationships (SARs) of NPs targeting specific proteins can be grasped. Under the guidance of co-crystal information, directional structural modification and simplification are powerful strategies for overcoming limitations of NPs, improving the success rate of NP-based drug discovery, and obtaining NP-based drugs with high selectivity, low toxicity and favorable pharmacokinetic characteristics. Here, we review the co-crystal information of a selection of NPs, focusing on the SARs of NPs reflected by co-crystal information and the modification and simplification strategies of NPs, and discuss how to apply co-crystal information in the optimization of NP-based lead compound.
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Affiliation(s)
- Xing Chen
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China; School of Public Health, Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, PR China.
| | - Swapna Varghese
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Zhaoyan Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Juncheng Du
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Banfeng Ruan
- Key Lab of Biofabrication of Anhui Higher Education, Hefei University, Hefei, 230601, PR China.
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Xinhua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
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2
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Heterocyclic Compounds as Hsp90 Inhibitors: A Perspective on Anticancer Applications. Pharmaceutics 2022; 14:pharmaceutics14102220. [PMID: 36297655 PMCID: PMC9610671 DOI: 10.3390/pharmaceutics14102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
Heat shock proteins (Hsps) have garnered special attention in cancer therapy as molecular chaperones with regulatory/mediatory effects on folding, maintenance/stability, maturation, and conformation of proteins as well as their effects on prevention of protein aggregation. Hsp90 ensures the stability of various client proteins needed for the growth of cells or the survival of tumor cells; therefore, they are overexpressed in tumor cells and play key roles in carcinogenesis. Accordingly, Hsp90 inhibitors are recognized as attractive therapeutic agents for investigations pertaining to tumor suppression. Natural Hsp90 inhibitors comprising geldanamycin (GM), reclaimed analogs of GM including 17-AAG and DMAG, and radicicol, a natural macrocyclic antifungal, are among the first potent Hsp90 inhibitors. Herein, recently synthesized heterocyclic compounds recognized as potent Hsp90 inhibitors are reviewed along with the anticancer effects of heterocyclic compounds, comprising purine, pyrazole, triazine, quinolines, coumarin, and isoxazoles molecules.
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3
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Pan- and isoform-specific inhibition of Hsp90: Design strategy and recent advances. Eur J Med Chem 2022; 238:114516. [DOI: 10.1016/j.ejmech.2022.114516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/11/2022]
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4
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Liang Y, Fang R, Rao Q. An Insight into the Medicinal Chemistry Perspective of Macrocyclic Derivatives with Antitumor Activity: A Systematic Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092837. [PMID: 35566196 PMCID: PMC9100616 DOI: 10.3390/molecules27092837] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
The profound pharmacological properties of macrocyclic compounds have led to their development as drugs. In conformationally pre-organized ring structures, the multiple functions and stereochemical complexity provided by the macrocycle result in high affinity and selectivity of protein targets while maintaining sufficient bioavailability to reach intracellular locations. Therefore, the construction of macrocycles is an ideal choice to solve the problem of “undruggable” targets. Inspection of 68 macrocyclic drugs on the market showed that 10 of them were used to treat cancer, but this structural class still has been poorly explored within drug discovery. This perspective considers the macrocyclic compounds used for anti-tumor with different targets, their advantages and disadvantages, and the various synthetic methods of them.
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Affiliation(s)
| | | | - Qiu Rao
- Correspondence: (Y.L.); (Q.R.)
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5
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Ohminato N, Nagayasu M, Ozeki K, Saitoh R, Ono N, Shibahara N, Suda A, Yoshinari K. In vivo- in vitro correlation of antitumor activity of heat shock protein 90 (HSP90) inhibitors with a pharmacokinetics/pharmacodynamics analysis using NCI-N87 xenograft mice. Xenobiotica 2021; 51:968-976. [PMID: 34134599 DOI: 10.1080/00498254.2021.1942588] [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: 10/21/2022]
Abstract
The in vitro antitumor activity (e.g. IC50) of anticancer drugs is important for selecting candidate compounds for in vivo drug efficacy study in the early stage of drug discovery. In this study, we investigated the relationship between in vitro IC50 and in vivo EC50 using six heat shock protein 90 (HSP90) inhibitors.IC50 of each compound was calculated from in vitro cell proliferation assays using the NCI-N87 cancer cell line. Each compound was administered to NCI-N87 xenograft mice, and EC50 and the maximum tumour-killing rate constant were calculated from pharmacokinetics/pharmacodynamics analyses using plasma concentrations and tumour volumes.IC50 obtained in vitro was poorly correlated with EC50 obtained in vivo, while a good correlation (r = 0.856) was observed between them when corrected with the unbound fraction ratio.The results of this study using of HSP90 inhibitors as model compounds suggest importance of the consideration of an unbound fraction to evaluate the relationship between IC50 and EC50. These results will contribute to improvement in the prediction accuracy of in vivo drug efficacy from in vitro activity and the efficiency of drug discovery research.
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Affiliation(s)
- Noriaki Ohminato
- Chugai Research Institute for Medical Science, Inc., Gotemba, Shizuoka, Japan.,Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Miho Nagayasu
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Kazuhisa Ozeki
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Ryoichi Saitoh
- Research Division, Chugai Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan; f Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Naomi Ono
- Research Division, Chugai Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan; f Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Norihito Shibahara
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Atsushi Suda
- Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Kouichi Yoshinari
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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6
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Zou J, Li Z, Liu S, Peng C, Fang D, Wan X, Lin Z, Lee TS, Raleigh DP, Yang M, Simmerling C. Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. J Chem Theory Comput 2021; 17:3710-3726. [PMID: 34029468 PMCID: PMC8215533 DOI: 10.1021/acs.jctc.1c00214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In silico screening of drug-target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings, and the introduction of cyclic structures from acyclic structures are commonly applied by medicinal chemists to improve binding affinity and enhance favorable properties of candidate compounds. These processes, commonly referred to as scaffold hopping, are challenging to model computationally. Although relative binding free energy (RBFE) calculations have shown success in predicting binding affinity changes caused by perturbing R-groups attached to a common scaffold, applications of RBFE calculations to modeling scaffold hopping are relatively limited. Scaffold hopping inevitably involves breaking and forming bond interactions of quadratic functional forms, which is highly challenging. A novel method for handling ring opening/closure/contraction/expansion and linker contraction/expansion is presented here. To the best of our knowledge, RBFE calculations on linker contraction/expansion have not been previously reported. The method uses auxiliary restraints to hold the atoms at the ends of a bond in place during the breaking and forming of the bonds. The broad applicability of the method was demonstrated by examining perturbations involving small-molecule macrocycles and mutations of proline in proteins. High accuracy was obtained using the method for most of the perturbations studied. The rigor of the method was isolated from the force field by validating the method using relative and absolute hydration free energy calculations compared to standard simulation results. Unlike other methods that rely on λ-dependent functional forms for bond interactions, the method presented here can be employed using modern molecular dynamics software without modification of codes or force field functions.
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Affiliation(s)
- Junjie Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Zhipeng Li
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Shuai Liu
- XtalPi Inc., 245 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Dong Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Xiao Wan
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey, 08854-8076, United States
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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7
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Amrhein JA, Knapp S, Hanke T. Synthetic Opportunities and Challenges for Macrocyclic Kinase Inhibitors. J Med Chem 2021; 64:7991-8009. [PMID: 34076436 DOI: 10.1021/acs.jmedchem.1c00217] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Macrocycles are typically cyclic variants of inhibitors derived from uncyclized canonical molecules or from natural products. For medicinal chemistry, drug-like macrocycles have received increasing interest over the past few years, since it has been demonstrated that macrocyclization can favorably alter the biological and physiochemical properties as well as selectivity in comparison to the acyclic analogue. Recent drug approvals such as Lorlatinib, glecaprevir, or voxilaprevir underline the clinical relevance of drug-like macrocycles. However, the synthesis of drug-like macrocycles can be challenging, since the ring-closing reaction is generally challenging with yields depending on the size and geometry of the bridging linker. Nevertheless, macrocycles are one opportunity to expand the synthetic toolbox for medicinal chemistry to provide bioactive molecules. Therefore, we reviewed the past literature of drug-like macrocycles highlighting reactions that have been successfully used for the macrocyclization. We classified the cyclization reactions by their type, ring-size, yield, and macrocyclization efficiency index.
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Affiliation(s)
- Jennifer Alisa Amrhein
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structure Genomics Consortium Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structure Genomics Consortium Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structure Genomics Consortium Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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8
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Abstract
Background:
This review presents the exhaustive exploration of 1,3,5-triazine scaffold
for development of analogs of anticancer drugs, over the last century. In the recent years, striazine
moiety has been one of the most studied moiety, showing broad-spectrum pharmacological
activities such as antibacterial, antifungal, analgesic, anti-HIV, antileishmanial, antitrypanosomal,
antimalarial and antiviral. Nowadays, many boffins are have become interested in novel
synthesis of s-triazine derivatives because of low cost and ease of availability.
Methods:
This scaffold has been extensively investigated mainly in the past decade. Many products
have been synthesized from different starting materials and these synthetic products possess
anticancer potential against various cell lines.
Results:
Many 1,3,5-triazine analogs exhibited significant anticancer activity in various models
and cell lines exhibiting different mechanisms. Some analogs have also shown good pharmacokinetic
parameters with less IC50 values.
Conclusion:
Various 1,3,5-triazine analogs have shown potent activities and may be regarded as
clinical candidates for future anticancer formulations. This review may be helpful to those researchers
seeking required information with regard to the drug design and medicinal properties of
1,3,5-triazine derivatives for selected targets. This review may also offer help to find and improve
clinically viable anticancer molecules.
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Affiliation(s)
- Rajeev Kumar
- Devsthali Vidyapeeth College of Pharmacy, Lalpur, Rudrapur (U.S. Nagar)-263148, Uttarakhand, India
| | - Neeraj Kumar
- Devsthali Vidyapeeth College of Pharmacy, Lalpur, Rudrapur (U.S. Nagar)-263148, Uttarakhand, India
| | | | - Anita Singh
- Department of Pharmacy, Kumaun University, Bhimtal, Nainital-263136, Uttarakhand, India
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9
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Mettu A, Talla V, Bajaj DM, Subhashini NJP. Design, synthesis, and molecular docking studies of novel pyrazolyl 2-aminopyrimidine derivatives as HSP90 inhibitors. Arch Pharm (Weinheim) 2019; 352:e1900063. [PMID: 31411362 DOI: 10.1002/ardp.201900063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 01/16/2023]
Abstract
A series of novel pyrazolyl 2-aminopyrimidine derivatives (7a-t) were designed based on scaffold hopping techniques, synthesized and biologically evaluated for their HSP90 inhibition and anticancer activity. Several compounds exhibited potent HSP90 inhibition with IC50 values less than that of the reference standard 17-AAG (1.25 µM). The most potent compound 7t displayed excellent HSP90 inhibition with an IC50 of 20 nM and in vitro antiproliferative potential against three cancer cell lines (IC50 < 5 µM). 7t also induced dose dependent degradation of client proteins (pHER2 and pERK1/2) in Western blot analysis. Several structural features of 7p-t oriented the molecules to retain all the essential binding interactions with HSP90, as observed by rationalized docking studies. Therefore, the para-nitrophenyl ring on the central pyrazole ring along with the 2-amino group on the pyrimidine ring are the crucial features in the development of novel HSP90 inhibitors based on this scaffold for targeted anticancer therapy.
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Affiliation(s)
- Akhila Mettu
- Department of Pharmaceutical Chemistry, Gokaraju Rangaraju College of Pharmacy, Kukatpally, Hyderabad, India
| | - Venu Talla
- Department of Pharmacology, National Institute of Pharmaceutical Education and Research, Balanagar, Hyderabad, India
| | - Deepti Madanlal Bajaj
- Department of Pharmacology, National Institute of Pharmaceutical Education and Research, Balanagar, Hyderabad, India
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10
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Wang T, Rodina A, Dunphy MP, Corben A, Modi S, Guzman ML, Gewirth DT, Chiosis G. Chaperome heterogeneity and its implications for cancer study and treatment. J Biol Chem 2018; 294:2162-2179. [PMID: 30409908 DOI: 10.1074/jbc.rev118.002811] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The chaperome is the collection of proteins in the cell that carry out molecular chaperoning functions. Changes in the interaction strength between chaperome proteins lead to an assembly that is functionally and structurally distinct from each constituent member. In this review, we discuss the epichaperome, the cellular network that forms when the chaperome components of distinct chaperome machineries come together as stable, functionally integrated, multimeric complexes. In tumors, maintenance of the epichaperome network is vital for tumor survival, rendering them vulnerable to therapeutic interventions that target critical epichaperome network components. We discuss how the epichaperome empowers an approach for precision medicine cancer trials where a new target, biomarker, and relevant drug candidates can be correlated and integrated. We introduce chemical biology methods to investigate the heterogeneity of the chaperome in a given cellular context. Lastly, we discuss how ligand-protein binding kinetics are more appropriate than equilibrium binding parameters to characterize and unravel chaperome targeting in cancer and to gauge the selectivity of ligands for specific tumor-associated chaperome pools.
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Affiliation(s)
- Tai Wang
- From the Chemical Biology Program and
| | | | | | - Adriana Corben
- the Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shanu Modi
- Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Monica L Guzman
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, and
| | - Daniel T Gewirth
- the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203
| | - Gabriela Chiosis
- From the Chemical Biology Program and .,Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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11
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Yu HS, Deng Y, Wu Y, Sindhikara D, Rask AR, Kimura T, Abel R, Wang L. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. J Chem Theory Comput 2017; 13:6290-6300. [PMID: 29120625 DOI: 10.1021/acs.jctc.7b00885] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.
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Affiliation(s)
- Haoyu S Yu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yujie Wu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Dan Sindhikara
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Amy R Rask
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Takayuki Kimura
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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12
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Wagner V, Jantz L, Briem H, Sommer K, Rarey M, Christ CD. Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation. ChemMedChem 2017; 12:1866-1872. [PMID: 28977738 PMCID: PMC5725703 DOI: 10.1002/cmdc.201700478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/26/2017] [Indexed: 12/21/2022]
Abstract
Macrocycles play an increasing role in drug discovery, but their synthesis is often demanding. Computational tools that suggest macrocyclization based on a known binding mode and that estimate the binding affinity of these macrocycles could have a substantial impact on the medicinal chemistry design process. For both tasks, we established a workflow with high practical value. For five diverse pharmaceutical targets we show that the effect of macrocyclization on binding can be calculated robustly and accurately. Applying this method to macrocycles designed by LigMac, a search tool for de novo macrocyclization, our results suggest that we have a robust protocol in hand to design macrocycles and prioritize them prior to synthesis.
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Affiliation(s)
- Vincent Wagner
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
| | - Linda Jantz
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Hans Briem
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
| | - Kai Sommer
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Matthias Rarey
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Clara D. Christ
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
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13
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Cascioferro S, Parrino B, Spanò V, Carbone A, Montalbano A, Barraja P, Diana P, Cirrincione G. 1,3,5-Triazines: A promising scaffold for anticancer drugs development. Eur J Med Chem 2017; 142:523-549. [PMID: 29046238 DOI: 10.1016/j.ejmech.2017.09.035] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
Abstract
This review covering literature reports from the beginning of this century to 2016 describes the synthetic pathways, the antitumor activity, the structure-activity relationship and, whenever reported, the possible mechanism of action of 1,3,5-triazine derivatives as well as of their hetero-fused compounds. Many 1,3,5-triazine derivatives, both uncondensed and hetero-fused, have shown remarkable antitumor activities and some of them reached clinical development.
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Affiliation(s)
- Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Carbone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy.
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Cleves AE, Jain AN. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. J Comput Aided Mol Des 2017; 31:419-439. [PMID: 28289981 PMCID: PMC5429375 DOI: 10.1007/s10822-017-0015-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/27/2017] [Indexed: 12/22/2022]
Abstract
We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.
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Affiliation(s)
- Ann E Cleves
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - Ajay N Jain
- Dept. of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA.
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15
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Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations. J Comput Aided Mol Des 2016; 30:707-730. [PMID: 27565797 PMCID: PMC5078160 DOI: 10.1007/s10822-016-9942-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/17/2016] [Indexed: 11/25/2022]
Abstract
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.
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Affiliation(s)
- Majda Misini Ignjatović
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
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HSP90 inhibitor CH5164840 induces micronuclei in TK6 cells via an aneugenic mechanism. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 773:9-13. [DOI: 10.1016/j.mrgentox.2014.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/08/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022]
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17
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Kanamaru C, Yamada Y, Hayashi S, Matsushita T, Suda A, Nagayasu M, Kimura K, Chiba S. Retinal toxicity induced by small-molecule Hsp90 inhibitors in beagle dogs. J Toxicol Sci 2014; 39:59-69. [DOI: 10.2131/jts.39.59] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
| | | | | | | | - Atsushi Suda
- Research Division, Chugai Pharmaceutical Co., Ltd
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18
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Saitoh R, Nagayasu M, Shibahara N, Ono N, Suda A, Kato M, Ishigai M. Assessing the Impact of HER2 Status on the Antitumor Activity of an HSP90 Inhibitor in Human Tumor Xenograft Mice Using Pharmacokinetic–Pharmacodynamic Modeling. Drug Metab Pharmacokinet 2014; 29:185-91. [DOI: 10.2133/dmpk.dmpk-13-rg-066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Ono N, Yamazaki T, Tsukaguchi T, Fujii T, Sakata K, Suda A, Tsukuda T, Mio T, Ishii N, Kondoh O, Aoki Y. Enhanced antitumor activity of erlotinib in combination with the Hsp90 inhibitor CH5164840 against non-small-cell lung cancer. Cancer Sci 2013; 104:1346-52. [PMID: 23863134 DOI: 10.1111/cas.12237] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 07/10/2013] [Accepted: 07/14/2013] [Indexed: 11/26/2022] Open
Abstract
Inhibition of heat shock protein 90 (Hsp90) can lead to degradation of multiple client proteins, which are involved in tumor progression. Epidermal growth factor receptor (EGFR) is one of the most potent oncogenic client proteins of Hsp90. Targeted inhibition of EGFR has shown clinical efficacy in the treatment of patients with non-small-cell lung cancer (NSCLC). However, primary and acquired resistance to the existing EGFR inhibitors is a major clinical problem. In the present study, we investigated the effect of the novel Hsp90 inhibitor CH5164840 on the antitumor activity of erlotinib. The NSCLC cell lines and xenograft models were treated with CH5164840 and erlotinib to examine their mechanisms of action and cell growth inhibition. We found that CH5164840 showed remarkable antitumor activity against NSCLC cell lines and xenograft models. The addition of CH5164840 enhanced the antitumor activity of erlotinib against NCI-H292 EGFR-overexpressing xenograft models. Phosphorylation of Stat3 increased with erlotinib treatment in NCI-H292 cells, which was abrogated by Hsp90 inhibition. Furthermore, in a NCI-H1975 T790M mutation erlotinib-resistant model, CH5164840 enhanced the antitumor activity of erlotinib despite the low efficacy of erlotinib treatment alone. In addition, ERK signaling was effectively suppressed by combination treatment with erlotinib and CH5164840 in a NCI-H1975 erlotinib-resistant model. Taken together, these data indicate that CH5164840 has potent antitumor activity and is highly effective in combination with erlotinib against NSCLC tumors with EGFR overexpression and mutations. Our results support the therapeutic potential of CH5164840 as a Hsp90 inhibitor for combination therapy with EGFR-targeting agents against EGFR-addicted NSCLC.
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Affiliation(s)
- Naomi Ono
- Discovery Pharmacology Department 2, Kamakura Research Laboratories, Chugai Pharmaceutical Co., Ltd, Kanagawa, Japan
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Targeting protein-protein interactions as an anticancer strategy. Trends Pharmacol Sci 2013; 34:393-400. [PMID: 23725674 DOI: 10.1016/j.tips.2013.04.007] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 02/07/2023]
Abstract
The emergence and convergence of cancer genomics, targeted therapies, and network oncology have significantly expanded the landscape of protein-protein interaction (PPI) networks in cancer for therapeutic discovery. Extensive biological and clinical investigations have led to the identification of protein interaction hubs and nodes that are critical for the acquisition and maintenance of characteristics of cancer essential for cell transformation. Such cancer-enabling PPIs have become promising therapeutic targets. With technological advances in PPI modulator discovery and validation of PPI-targeting agents in clinical settings, targeting of PPI interfaces as an anticancer strategy has become a reality. Future research directed at genomics-based PPI target discovery, PPI interface characterization, PPI-focused chemical library design, and patient-genomic subpopulation-driven clinical studies is expected to accelerate the development of the next generation of PPI-based anticancer agents for personalized precision medicine. Here we briefly review prominent PPIs that mediate cancer-acquired properties, highlight recognized challenges and promising clinical results in targeting PPIs, and outline emerging opportunities.
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Dong JF, Yu X, Ning CQ, Hu L, Yu NF. Selective mono-arylation in palladium-catalyzed cross-coupling reaction of dichlorotriazines with phenylboronate ester derivatives. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2012.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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