"Why didn't the company run a phase 3 trial on CKD instead of the CVD trial BETonMACE,...?"

The short answer is that Resverlogix would have had to start in Phase 1 or 2 for either the stage 3 CKD or end stage renal disease (ESRD) program, and could not go straight to Phase 3 for a renal program. See long answer below.

The New Zealand Phase 1 trial was small (8 normal patients, 8 ESRD patients) who received a single oral dose of 100 mg of apabetalone and who were then followed for 1 to 7 days. These patients had to have been previously diagnosed with ESRD and not on dialysis (eGFR <30 mL/min/1.73m2). So if Resverlogix wanted to pursue a Phase 3 trial in ESRD, they would have had to run more and larger Phase 1/2 trial(s) for both safety and efficacy before going into Phase 3. New Zealand published study is linked below.

Benefit of Apabetalone on Plasma Proteins in Renal Disease

ASSURE and SUSTAIN Phase 2 trials excluded patients with severe renal impairment (no ESRD patients). It was a small number of patients (13 placebo, 35 apabetalone) in the combined SUSTAIN and ASSURE analysis that qualified with the Stage 3 CKD eGFR <60 mL/min/1.73 m2. From the below publication "After combining data from the two trials, a total of 499 subjects received either 100mg b.i.d. of apabetalone (n=331) or placebo (n=168). In the SUSTAIN study, a total of 28 patients had baseline eGFR<60 mL/min/1.73 m2, with 18 randomized to the apabetalone group and 10 to the placebo group. In the ASSURE study, a total of 20 patients had baseline eGFR<60 mL/min/1.73 m2, with 17 randomized to the apabetalone group and 3 to the placebo group. A total of 48 patients were included in this post-hoc analysis." Furthermore, eGFR and alkaline phospatase changes were not pre-specified outcomes in either trial and was only tested in a post-hoc analysis that had marginal statistical significance (it was never designed or powered to be a CKD/eGFR study) as discussed here. So as stated for ESRD above, Resverlogix would have had to run more and larger Phase 1/2 trial(s) for both safety and efficacy in Stage 3 CKD patients before going into Phase 3. Combined SUSTAIN and ASSURE study linked below.

Apabetalone Mediated Epigenetic Modulation is Associated with Favorable Kidney Function and Alkaline Phosphatase Profile in Patients with Chronic Kidney Disease