Просто используйте подстроку:
datetimes <- c("2016-04-02 10:33:45 COT", "2016-04-02 22:19:24 COT" ,
"2016-04-09 17:47:13 COT", "2016-04-13 16:56:23 COT")
as.POSIXct(substring(datetimes, 1, nchar(datetimes[1])-7))
#[1] "2016-04-02 10:33:00 IST" "2016-04-02 22:19:00 IST"
# "2016-04-09 17:47:00 IST" "2016-04-13 16:56:00 IST"
# without timezone
format(substring(datetimes, 1, nchar(datetimes[1])-7),
format='%Y-%m-%d %H:%M:%S', usetz = FALSE)
#[1] "2016-04-02 10:33" "2016-04-02 22:19" "2016-04-09 17:47" "2016-04-13 16:56"