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 (
    86692, 86670, 86611, 86610, 86609, 86608, 
    87120, 86648, 87460, 87459, 87458, 
    87112, 86644, 86643, 86541, 87352, 
    87351, 87350, 87349, 87348, 87347, 
    87346, 87345, 87344, 87343, 87342, 
    87341, 87240, 87239, 87238, 87237, 
    87236, 87235, 87234, 87233, 87232, 
    87231, 87230, 87229, 87228
  ) 
  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 0.00122

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
86541 1.69000000
86608 1.69000000
86609 1.69000000
86610 1.69000000
86611 1.69000000
86643 1.69000000
86644 1.69000000
86648 1.69000000
86670 1.69000000
86692 1.69000000
87112 1.69000000
87120 1.69000000
87228 1.69000000
87229 1.69000000
87230 1.69000000
87231 1.69000000
87232 1.69000000
87233 1.69000000
87234 1.69000000
87235 1.69000000
87236 1.69000000
87237 1.69000000
87238 1.69000000
87239 1.69000000
87240 1.69000000
87341 1.69000000
87342 1.69000000
87343 1.69000000
87344 1.69000000
87345 1.69000000
87346 1.69000000
87347 1.69000000
87348 1.69000000
87349 1.69000000
87350 1.69000000
87351 1.69000000
87352 1.69000000
87458 1.69000000
87459 1.69000000
87460 1.69000000