SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    87227, 87226, 87225, 87224, 87223, 87222, 
    87221, 87220, 87219, 87218, 87217, 
    87216, 87000, 86999, 86998, 86997, 
    86996, 86995, 86994, 86993, 86506, 
    86447, 86446, 86445, 86444, 86384, 
    86383, 86382, 86381, 86380, 86379, 
    86378, 86377, 86376, 86375, 86374, 
    87116, 86470, 86469, 86468
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00102

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 80 Using where

Result

product_id price
86374 1.69000000
86375 1.69000000
86376 1.69000000
86377 1.69000000
86378 1.69000000
86379 1.69000000
86380 1.69000000
86381 1.69000000
86382 1.69000000
86383 1.69000000
86384 1.69000000
86444 1.69000000
86445 1.69000000
86446 1.69000000
86447 1.69000000
86468 1.69000000
86469 1.69000000
86470 1.69000000
86506 1.69000000
86993 1.69000000
86994 1.69000000
86995 1.69000000
86996 1.69000000
86997 1.69000000
86998 1.69000000
86999 1.69000000
87000 1.69000000
87116 1.69000000
87216 1.69000000
87217 1.69000000
87218 1.69000000
87219 1.69000000
87220 1.69000000
87221 1.69000000
87222 1.69000000
87223 1.69000000
87224 1.69000000
87225 1.69000000
87226 1.69000000
87227 1.69000000