If you have knee pain during any type of knee-flexed position, any lunge movement will cause it pain. I suggest a few things:
1.) Foam roll the hip flexors and quads. These will be very painful and discomforting at first. Foam roll daily (the first few days, you may find extreme soreness--but it will pass).
2.) Follow that with some stretching. Most desk workers, always leave the gym and attempt a "lunge" type movement at the gym--just as I depict in my
article. Stretch the entire lowerbody daily. Immediately after SMR is best.
3.) Next, attempt the knee to lunge drill. If that fails, I suggest moving to parallel bodyweight squats. Keep your arms extended in front of you ad focus on pushing the butt back. Your arms in front of you (chest height) will serve as a cantilever. Perform 12-15 reps. This will serve as a hip hinge mobility drill, that will prepare the muscles for the lunge.
If all else fails, see a medical professional. if you have chronic knee pain, take look at Mike Robertson's product, "Bulletproof Knees".