Phase 2 Study Adding Pracinostat to a Hypomethylating Agent (HMA) in Patients With MDS Who Failed to Respond to Single Agent HMA

Inclusion Criteria: 1. Voluntary written informed consent 2. Histologically or cytologically documented diagnosis of MDS (any French-American-British classification \[FAB\] subtype) 3. Bone marrow blasts \>5% and \<30% and a peripheral white blood cell (WBC) count of \<20,000 /µL 4. Bone marrow biopsy, aspirates, and peripheral blood smears within 28 days of first study treatment 5. Group 1: Primary failures: Progression after their most recent HMA therapy according to IWG criteria after receiving single agent azacitidine and/or single agent decitabine, or has worsening cytopenias (increased transfusion requirement), increased BM blasts, progression to a higher FAB type, or develops additional clinically significant cytogenetic abnormalities; Secondary failures: Relapse after any initial CR, PR, HI, or development of clinically significant cytogenetic abnormalities at any time according to IWG criteria after receiving single agent azacitidine or decitabine Group 2: Failure to achieve a response (any CR, PR or HI) according to IWG criteria definition of stable disease after the most recent HMA therapy (at least 6 cycles of azacitidine or 4 cycles of decitabine) 6. Must have demonstrated tolerability to single agent HMA 7. Able to start combination therapy within 3 months of the last single agent HMA dose with no other therapy for disease under study received during this interval 8. Not a candidate for hematopoietic stem cell transplant within 4 months of screening 9. ECOG performance status of 0, 1, or 2 10. Adequate organ function as evidenced by: * Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) ≤2.5 x the upper limit of normal (ULN) * Total bilirubin ≤1.5 x ULN or total bilirubin of ≤2 mg/dL, whichever is higher * Serum creatinine \<2 mg/dL, or creatinine clearance ≥60 mL/min * QTcF interval ≤470 msec 11. Female or male patients ≥18 years-of-age 12. Male patients with female partners are required to use two forms of acceptable contraception; Female patients of childbearing potential must have a negative pregnancy test ≤7 days before first study treatment. 13. Willingness and ability to understand the nature of this trial and to comply Exclusion Criteria: 1. Received any of the following within the specified time frame after the last single agent HMA dose until the first administration of study medication: * Any therapy for malignancy between the time of single agent HMA and first on-study treatment * Hydroxyurea within 48 hours prior to first study treatment * Hematopoietic growth factors: erythropoietin, granulocyte colony stimulating factor (G-CSF), granulocyte macrophage colony stimulating factor (GM-CSF), or thrombopoietin receptor agonists within 7 days (14 days for Aranesp) prior to first study treatment * Major surgery within 28 days of study day 1 2. Patients who are candidates for aggressive chemotherapy (e.g. typical AML induction therapy) 3. Cardiopulmonary function criteria: * Current unstable arrhythmia requiring treatment * History of symptomatic congestive heart failure (New York Heart Association Class III or IV) * History of myocardial infarction within 6 months of enrollment * Current unstable angina 4. Concomitant treatment with agents that have activity against HDAC inhibitors is not permitted 5. Clinical evidence of CNS involvement 6. Patients with gastrointestinal (GI) tract disease, uncontrolled inflammatory GI disease (e.g., Crohn's disease, ulcerative colitis) 7. Active infection with human immunodeficiency virus or chronic hepatitis B or C 8. Life-threatening illness unrelated to cancer or any serious medical or psychiatric illness that could potentially interfere with participation in this study 9. Presence of a malignant disease within the last 12 months, with the exception of adequately treated in-situ carcinomas, basal or squamous cell carcinoma, or non-melanomatous skin cancer and other concurrent malignancies will be considered on a case by case basis 10. Inability or unwillingness (including psychological, familial, sociological, or geographical conditions) to comply