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 (
    109465, 109886, 109742, 109741, 109740, 
    109739, 109448, 109447, 109446, 109445, 
    109444, 109376, 122293, 122292, 122291, 
    122290, 122289, 122288, 122287, 122286
  ) 
  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 0.00070

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 40 Using where

Result

product_id price
109376 1.69000000
109444 1.69000000
109445 1.69000000
109446 1.69000000
109447 1.69000000
109448 1.69000000
109465 1.69000000
109739 1.69000000
109740 1.69000000
109741 1.69000000
109742 1.69000000
109886 1.69000000
122286 1.69000000
122287 1.69000000
122288 1.69000000
122289 1.69000000
122290 1.69000000
122291 1.69000000
122292 1.69000000
122293 1.69000000