1
|
Berlow NE, Rikhi R, Geltzeiler M, Abraham J, Svalina MN, Davis LE, Wise E, Mancini M, Noujaim J, Mansoor A, Quist MJ, Matlock KL, Goros MW, Hernandez BS, Doung YC, Thway K, Tsukahara T, Nishio J, Huang ET, Airhart S, Bult CJ, Gandour-Edwards R, Maki RG, Jones RL, Michalek JE, Milovancev M, Ghosh S, Pal R, Keller C. Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma. BMC Cancer 2019; 19:593. [PMID: 31208434 PMCID: PMC6580486 DOI: 10.1186/s12885-019-5681-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/07/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cancer patients with advanced disease routinely exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when their disease inevitably progresses. To address the unmet clinical need for evidence-based therapy assignment when standard clinical approaches have failed, we have developed a probabilistic computational modeling approach which integrates molecular sequencing data with functional assay data to develop patient-specific combination cancer treatments. METHODS Tissue taken from a murine model of alveolar rhabdomyosarcoma was used to perform single agent drug screening and DNA/RNA sequencing experiments; results integrated via our computational modeling approach identified a synergistic personalized two-drug combination. Cells derived from the primary murine tumor were allografted into mouse models and used to validate the personalized two-drug combination. Computational modeling of single agent drug screening and RNA sequencing of multiple heterogenous sites from a single patient's epithelioid sarcoma identified a personalized two-drug combination effective across all tumor regions. The heterogeneity-consensus combination was validated in a xenograft model derived from the patient's primary tumor. Cell cultures derived from human and canine undifferentiated pleomorphic sarcoma were assayed by drug screen; computational modeling identified a resistance-abrogating two-drug combination common to both cell cultures. This combination was validated in vitro via a cell regrowth assay. RESULTS Our computational modeling approach addresses three major challenges in personalized cancer therapy: synergistic drug combination predictions (validated in vitro and in vivo in a genetically engineered murine cancer model), identification of unifying therapeutic targets to overcome intra-tumor heterogeneity (validated in vivo in a human cancer xenograft), and mitigation of cancer cell resistance and rewiring mechanisms (validated in vitro in a human and canine cancer model). CONCLUSIONS These proof-of-concept studies support the use of an integrative functional approach to personalized combination therapy prediction for the population of high-risk cancer patients lacking viable clinical options and without actionable DNA sequencing-based therapy.
Collapse
Affiliation(s)
- Noah E. Berlow
- Children’s Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR 97005 USA
- Electrical and Computer Engineering, Texas Tech University, Lubbock, TX 79409 USA
| | - Rishi Rikhi
- Children’s Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR 97005 USA
| | - Mathew Geltzeiler
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239 USA
- Department of Otolaryngology – Head and Neck Surgery, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jinu Abraham
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Matthew N. Svalina
- Children’s Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR 97005 USA
| | - Lara E. Davis
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239 USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA
| | - Erin Wise
- Champions Oncology, Baltimore, MD 21205 USA
| | | | - Jonathan Noujaim
- Royal Marsden Hospital and Institute of Cancer Research, London, SW3 6JJ UK
- Hôpital Maisonneuve-Rosemont, Montreal, H1T 2M4 Canada
| | - Atiya Mansoor
- Department of Pathology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Michael J. Quist
- Center for Spatial Systems Biomedicine Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Kevin L. Matlock
- Electrical and Computer Engineering, Texas Tech University, Lubbock, TX 79409 USA
- Omics Data Automation, 12655 SW Beaverdam Road, Beaverton, OR 97005 USA
| | - Martin W. Goros
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, TX 78229 USA
| | - Brian S. Hernandez
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, TX 78229 USA
| | - Yee C. Doung
- Department of Orthopedic Surgery, Oregon Health & Science University, Portland, OR 97239 USA
| | - Khin Thway
- Royal Marsden Hospital and Institute of Cancer Research, London, SW3 6JJ UK
| | - Tomohide Tsukahara
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, 060-8556 Japan
| | - Jun Nishio
- Department of Orthopaedic Surgery, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Elaine T. Huang
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239 USA
| | | | | | - Regina Gandour-Edwards
- Department of Pathology & Laboratory Medicine, UC Davis Health System, Sacramento, CA 95817 USA
| | - Robert G. Maki
- Sarcoma Program, Zucker School of Medicine at Hofstra/Northwell & Cold Spring Harbor Laboratory, Long Island, NY 10142 USA
| | - Robin L. Jones
- Royal Marsden Hospital and Institute of Cancer Research, London, SW3 6JJ UK
| | - Joel E. Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, TX 78229 USA
| | - Milan Milovancev
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA
| | - Souparno Ghosh
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79409 USA
| | - Ranadip Pal
- Electrical and Computer Engineering, Texas Tech University, Lubbock, TX 79409 USA
| | - Charles Keller
- Children’s Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR 97005 USA
| |
Collapse
|
6
|
Ohlmeyer M, Zhou MM. Integration of small-molecule discovery in academic biomedical research. ACTA ACUST UNITED AC 2011; 77:350-7. [PMID: 20687180 DOI: 10.1002/msj.20197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Rapid advances in biomedical sciences in recent years have drastically accelerated the discovery of the molecular basis of human diseases. The great challenge is how to translate the newly acquired knowledge into new medicine for disease prevention and treatment. Drug discovery is a long and expensive process, and the pharmaceutical industry has not been very successful at it, despite its enormous resources and spending on the process. It is increasingly realized that academic biomedical research institutions ought to be engaged in early-stage drug discovery, especially when it can be coupled to their basic research. To leverage the productivity of new-drug development, a substantial acceleration in validation of new therapeutic targets is required, which would require small molecules that can precisely control target functions in complex biological systems in a temporal and dose-dependent manner. In this review, we describe a process of integration of small-molecule discovery and chemistry in academic biomedical research that will ideally bring together the elements of innovative approaches to new molecular targets, existing basic and clinical research, screening infrastructure, and synthetic and medicinal chemistry to follow up on small-molecule hits. Such integration of multidisciplinary resources and expertise will enable academic investigators to discover novel small molecules that are expected to facilitate their efforts in both mechanistic research and new-drug target validation. More broadly academic drug discovery should contribute new entities to therapy for intractable human diseases, especially for orphan diseases, and hopefully stimulate and synergize with the commercial sector.
Collapse
Affiliation(s)
- Michael Ohlmeyer
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY, USA
| | | |
Collapse
|
7
|
Duplantier AJ, Efremov I, Candler J, Doran AC, Ganong AH, Haas JA, Hanks AN, Kraus KG, Lazzaro JT, Lu J, Maklad N, McCarthy SA, O'Sullivan TJ, Rogers BN, Siuciak JA, Spracklin DK, Zhang L. 3-Benzyl-1,3-oxazolidin-2-ones as mGluR2 positive allosteric modulators: Hit-to lead and lead optimization. Bioorg Med Chem Lett 2009; 19:2524-9. [PMID: 19328692 DOI: 10.1016/j.bmcl.2009.03.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 03/09/2009] [Accepted: 03/10/2009] [Indexed: 11/15/2022]
Abstract
The discovery, synthesis and SAR of a novel series of 3-benzyl-1,3-oxazolidin-2-ones as positive allosteric modulators (PAMs) of mGluR2 is described. Expedient hit-to-lead work on a single HTS hit led to the identification of a ligand-efficient and structurally attractive series of mGluR2 PAMs. Human microsomal clearance and suboptimal physicochemical properties of the initial lead were improved to give potent, metabolically stable and orally available mGluR2 PAMs.
Collapse
Affiliation(s)
- Allen J Duplantier
- CNS Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
The influence of lead discovery strategies on the properties of drug candidates. Nat Rev Drug Discov 2009; 8:203-12. [PMID: 19247303 DOI: 10.1038/nrd2796] [Citation(s) in RCA: 441] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite the widespread acceptance of guidelines related to desirable physicochemical properties of potential small-molecule drugs, key properties - such as lipophilicity - of recently developed clinical candidates and advanced lead compounds have been shown to differ significantly from those of historical leads and drugs. By analysing the physicochemical properties of a large database of hits and corresponding leads identified in the past decade, we show that this undesirable phenomenon can be traced back to the nature of high-throughput screening hits and hit-to-lead optimization practices. Conceptual and organizational adjustments may be required to enable a smooth lead-evolution process that reduces the chance of high compound-related attrition in clinical trials.
Collapse
|
9
|
Zinner RG, Barrett BL, Popova E, Damien P, Volgin AY, Gelovani JG, Lotan R, Tran HT, Pisano C, Mills GB, Mao L, Hong WK, Lippman SM, Miller JH. Algorithmic guided screening of drug combinations of arbitrary size for activity against cancer cells. Mol Cancer Ther 2009; 8:521-32. [PMID: 19276160 DOI: 10.1158/1535-7163.mct-08-0937] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The standard treatment for most advanced cancers is multidrug therapy. Unfortunately, combinations in the clinic often do not perform as predicted. Therefore, to complement identifying rational drug combinations based on biological assumptions, we hypothesized that a functional screen of drug combinations, without limits on combination sizes, will aid the identification of effective drug cocktails. Given the myriad possible cocktails and inspired by examples of search algorithms in diverse fields outside of medicine, we developed a novel, efficient search strategy called Medicinal Algorithmic Combinatorial Screen (MACS). Such algorithms work by enriching for the fitness of cocktails, as defined by specific attributes through successive generations. Because assessment of synergy was not feasible, we developed a novel alternative fitness function based on the level of inhibition and the number of drugs. Using a WST-1 assay on the A549 cell line, through MACS, we screened 72 combinations of arbitrary size formed from a 19-drug pool across four generations. Fenretinide, suberoylanilide hydroxamic acid, and bortezomib (FSB) was the fittest. FSB performed up to 4.18 SD above the mean of a random set of cocktails or "too well" to have been found by chance, supporting the utility of the MACS strategy. Validation studies showed FSB was inhibitory in all 7 other NSCLC cell lines tested. It was also synergistic in A549, the one cell line in which this was evaluated. These results suggest that when guided by MACS, screening larger drug combinations may be feasible as a first step in combination drug discovery in a relatively small number of experiments.
Collapse
Affiliation(s)
- Ralph G Zinner
- Department of Thoracic/Head and Neck Medical Oncology, Unit 432, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|