A unique small molecule pair controls the plant circadian clock

Circadian clocks are the biological time keeping systems that coordinate genetic, metabolic, and physiological behaviors with the external day-night cycle. Previous studies have suggested possible molecular mechanisms for the circadian clock in Arabidopsis thaliana (Arabidopsis), but there might be additional mechanisms that have been hidden due to genetic redundancy. A clock reporter line of Arabidopsis was screened against the 10,000 chemicals in the Maybridge Hitfinder10K chemical library, and a structure-activity relationship study of hit compounds was conducted. Clock mutants were treated with two of the small molecules to gain insight into their mode of action. The screening identified 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidine-4,6(5H)-dione (TU-892) as a period lengthening molecule. From a structure-activity relationship study, we found that a molecule possessing 2,4-dichlorophenyl instead of a 3,4-dichlorophenyl group (TU-923) had period shortening activity. The period shortening activity of TU-923 was reversed to a lengthening activity in double mutants lacking PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7 (prr9-10 prr7-11). Our study provides a unique small molecule pair that regulates the pace of the clock in opposite ways, likely by targeting unknown factors. Small differences at the atomic level can reverse the period tuning activities. PRR9 and PRR7 are essential for the activity of TU-923 in period shortening.