4
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Egbert M, Whitty A, Keserű GM, Vajda S. Why Some Targets Benefit from beyond Rule of Five Drugs. J Med Chem 2019; 62:10005-10025. [PMID: 31188592 DOI: 10.1021/acs.jmedchem.8b01732] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Beyond rule-of-five (bRo5) compounds are increasingly used in drug discovery. Here we analyze 37 target proteins that have bRo5 drugs or clinical candidates. Targets can benefit from bRo5 drugs if they have "complex" hot spot structure with four or more hots spots, including some strong ones. Complex I targets show positive correlation between binding affinity and molecular weight. These targets are conventionally druggable, but reaching additional hot spots enables improved pharmaceutical properties. Complex II targets, mostly protein kinases, also have strong hot spots but show no correlation between affinity and ligand molecular weight, and the primary motivation for creating larger drugs is to increase selectivity. Each target considered as complex III has some specific reason for requiring bRo5 drugs. Finally, targets with "simple" hot spot structure, i.e., three or fewer weak hot spots, must use larger compounds that interact with surfaces beyond the hot spot region to achieve acceptable affinity.
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Affiliation(s)
- Megan Egbert
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Adrian Whitty
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Center for Natural Sciences , Magyar Tudósok krt. 2 , H-1117 Budapest , Hungary
| | - Sandor Vajda
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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5
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Ansar S, Sadhasivam A, Vetrivel U. PocketPipe: A computational pipeline for integratedPocketome prediction and comparison. Bioinformation 2019; 15:295-298. [PMID: 31285647 PMCID: PMC6599441 DOI: 10.6026/97320630015295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 01/03/2023] Open
Abstract
Functional characterisation of proteins often depends on specific interactions with other molecules. In the drug discovery scenario, the
ability of a protein to bind with drug-like molecule with a high affinity is referred as druggability. Deciphering such druggable binding
pockets on proteins plays an important role in structure-based drug designing studies. Moreover, availability of plethora of structural data
poses a need automated pipelines which can efficiently integrate robust algorithms towards large-scale pocket identification and
comparison. These pipelines have direct applicability on off-target analysis, drug repurposing and structural prioritization of drug targets
in pathogenic microbes. However, currently there is a paucity of such efficient pipelines. Hence, by this study a highly optimized shell
script based pipeline (PocketPipe) has been developed with seamless integration of robust algorithms namely, P2Rank (predicts binding
sites based on machine learning) and PocketMatch-v2.1 (compares binding pockets by residue-based method), for pocketome generation
and comparison, respectively. The process of input workflow and various steps carried out by PocketPipe and the output results are well
documented in the operating manual. On execution, the pipeline features seamless operability, high scalability, dynamic file handling and
results parsing. PocketPipe is distributed freely under GNU GPL license and can be downloaded at
https://github.com/inpacdb/PocketPipe
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Affiliation(s)
- Samdani Ansar
- 1Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, SankaraNethralaya, Chennai - 600 006, Tamil Nadu, India.,2School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Anupriya Sadhasivam
- 1Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, SankaraNethralaya, Chennai - 600 006, Tamil Nadu, India
| | - Umashankar Vetrivel
- 1Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, SankaraNethralaya, Chennai - 600 006, Tamil Nadu, India
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6
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Abbott KL, Chaudhury CS, Chandran A, Vishveshwara S, Dvorak Z, Jiskrova E, Poulikova K, Vyhlidalova B, Mani S, Pondugula SR. Belinostat, at Its Clinically Relevant Concentrations, Inhibits Rifampicin-Induced CYP3A4 and MDR1 Gene Expression. Mol Pharmacol 2019; 95:324-334. [PMID: 30622215 PMCID: PMC6362450 DOI: 10.1124/mol.118.114587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/03/2019] [Indexed: 01/26/2023] Open
Abstract
Activation of human pregnane X receptor (hPXR) has been associated with induction of chemoresistance. It has been proposed that such chemoresistance via cytochrome P450/drug transporters can be reversed with the use of antagonists that specifically abrogate agonist-mediated hPXR activation. Unfortunately, proposed antagonists lack the specificity and appropriate pharmacological characteristics that allow these features to be active in the clinic. We propose that, ideally, an hPXR antagonist would be a cancer drug itself that is part of a "cancer drug cocktail" and effective as an hPXR antagonist at therapeutic concentrations. Belinostat (BEL), a histone deacetylase inhibitor approved for the treatment of relapsed/refractory peripheral T-cell lymphoma, and often used in combination with chemotherapy, is an attractive candidate based on its hPXR ligand-like features. We sought to determine whether these features of BEL might allow it to behave as an antagonist in combination chemotherapy regimens that include hPXR activators. BEL represses agonist-activated hPXR target gene expression at its therapeutic concentrations in human primary hepatocytes and LS174T human colon cancer cells. BEL repressed rifampicin-induced gene expression of CYP3A4 and multidrug resistance protein 1, as well as their respective protein activities. BEL decreased rifampicin-induced resistance to SN-38, the active metabolite of irinotecan, in LS174T cells. This finding indicates that BEL could suppress hPXR agonist-induced chemoresistance. BEL attenuated the agonist-induced steroid receptor coactivator-1 interaction with hPXR, and, together with molecular docking studies, the study suggests that BEL directly interacts with multiple sites on hPXR. Taken together, our results suggest that BEL, at its clinically relevant therapeutic concentration, can antagonize hPXR agonist-induced gene expression and chemoresistance.
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Affiliation(s)
- Kodye L Abbott
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Chloe S Chaudhury
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Aneesh Chandran
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Saraswathi Vishveshwara
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Zdenek Dvorak
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Eva Jiskrova
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Karolina Poulikova
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Barbora Vyhlidalova
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Sridhar Mani
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
| | - Satyanarayana R Pondugula
- Department of Anatomy, Physiology and Pharmacology (K.L.A., C.S.C., S.R.P.) and Auburn University Research Initiative in Cancer (K.L.A., C.S.C., S.R.P.), Auburn University, Auburn, Alabama; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (A.C., S.V.); Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic (Z.D., E.J., K.P., B.V.); and Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, New York (S.M.)
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8
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Srinivasan B, Tonddast-Navaei S, Skolnick J. Pocket detection and interaction-weighted ligand-similarity search yields novel high-affinity binders for Myocilin-OLF, a protein implicated in glaucoma. Bioorg Med Chem Lett 2017; 27:4133-4139. [PMID: 28739043 DOI: 10.1016/j.bmcl.2017.07.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
Traditional structure and ligand based virtual screening approaches rely on the availability of structural and ligand binding information. To overcome this limitation, hybrid approaches were developed that relied on extraction of ligand binding information from proteins sharing similar folds and hence, evolutionarily relationship. However, they cannot target a chosen pocket in a protein. To address this, a pocket centric virtual ligand screening approach is required. Here, we employ a new, iterative implementation of a pocket and ligand-similarity based approach to virtual ligand screening to predict small molecule binders for the olfactomedin domain of human myocilin implicated in glaucoma. Small-molecule binders of the protein might prevent the aggregation of the protein, commonly seen during glaucoma. First round experimental assessment of the predictions using differential scanning fluorimetry with myoc-OLF yielded 7 hits with a success rate of 12.7%; the best hit had an apparent dissociation constant of 99nM. By matching to the key functional groups of the best ligand that were likely involved in binding, the affinity of the best hit was improved by almost 10,000 fold from the high nanomolar to the low picomolar range. Thus, this study provides preliminary validation of the methodology on a medically important glaucoma associated protein.
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Affiliation(s)
- Bharath Srinivasan
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950, Atlantic Drive, Atlanta, GA 30332, United States
| | - Sam Tonddast-Navaei
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950, Atlantic Drive, Atlanta, GA 30332, United States
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950, Atlantic Drive, Atlanta, GA 30332, United States.
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9
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Srinivasan B, Rodrigues JV, Tonddast-Navaei S, Shakhnovich E, Skolnick J. Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants. ACS Chem Biol 2017; 12:1848-1857. [PMID: 28525268 DOI: 10.1021/acschembio.7b00175] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug discovery, systematic variations of substituents on a common scaffold and bioisosteric replacements are often used to generate diversity and obtain molecules with better biological effects. However, this could saturate the small-molecule diversity pool resulting in drug resistance. On the other hand, conventional drug discovery relies on targeting known pockets on protein surfaces leading to drug resistance by mutations of critical pocket residues. Here, we present a two-pronged strategy of designing novel drugs that target unique pockets on a protein's surface to overcome the above problems. Dihydrofolate reductase, DHFR, is a critical enzyme involved in thymidine and purine nucleotide biosynthesis. Several classes of compounds that are structural analogues of the substrate dihydrofolate have been explored for their antifolate activity. Here, we describe 10 novel small-molecule inhibitors of Escherichia coli DHFR, EcDHFR, belonging to the stilbenoid, deoxybenzoin, and chalcone family of compounds discovered by a combination of pocket-based virtual ligand screening and systematic scaffold hopping. These inhibitors show a unique uncompetitive or noncompetitive inhibition mechanism, distinct from those reported for all known inhibitors of DHFR, indicative of binding to a unique pocket distinct from either substrate or cofactor-binding pockets. Furthermore, we demonstrate that rescue mutants of EcDHFR, with reduced affinity to all known classes of DHFR inhibitors, are inhibited at the same concentration as the wild-type. These compounds also exhibit antibacterial activity against E. coli harboring the drug-resistant variant of DHFR. This discovery is the first report on a novel class of inhibitors targeting a unique pocket on EcDHFR.
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Affiliation(s)
- Bharath Srinivasan
- Center
for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - João V. Rodrigues
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Sam Tonddast-Navaei
- Center
for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Eugene Shakhnovich
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Jeffrey Skolnick
- Center
for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
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